I had my water tested but need explanation

Paul B

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AquaBiomics tested my water a few weeks ago and I am all excited to know what it means as I can't interpret most of it so I need Randy who has more degrees than a thermometer, and I am an electrician with a fish tank.

Years ago I couldn't spell Lectrician but now I are one.
 

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redfishbluefish

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@Paul B , unfortunately I'm not going to be able to add much to this discussion. However, we always knew you were different, but now we have proof.....that you are only 12% balanced! :eek:
Paul B Balance.png


I do have to thank you in that I did not know this service was available....very interesting results. That said, I'd like to see a similar test done on the waters of Long Island Sound....where you collect your water and sludge. The only info I can add to this discussion is that I do know that certain bacteria is temperature/seasonally varied, so that dependent on when you collect, you'll get considerably different percentages of populations. So maybe part of the reason you're seeing varied populations is that you're collecting your water from a temperate water source.

The other thought is how polluted is the Sound? And were is the closest outflow from a sewage treatment plant?
 

brandon429

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Does the multi decade health and production from Pauls system have any weight compared to the measure that a microbial species is lacking

If those species deemed lacking are boosted, what will be the impact in the tank claimed, how can the measures be put to use or aid recourse—-what is actually wrong with the tank given the measure? Would we think anything is wrong with the tank other than the bac testing
 

Idoc

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That is a real interesting test that I didn't know existed!
 

AquaBiomics

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AquaBiomics tested my water a few weeks ago and I am all excited to know what it means as I can't interpret most of it so I need Randy who has more degrees than a thermometer, and I am an electrician with a fish tank.

Years ago I couldn't spell Lectrician but now I are one.
Hi Paul,

Here are my thoughts on the microbiome of your famous aquarium, the most mature reef tank I've yet had the privilege of testing. Both your water and biofilm samples contained plenty of DNA so these conclusions are based on analysis of thousands of high quality DNA sequences from your sample.

First the diversity (which is simply the number of different kinds of microbes found in your sample). Your tank was more diverse than 2/3 of those I sampled. This is even more impressive when you consider its age. Older tanks tend to have lower diversity ... tanks <5 years old ranged from about 100 to over 600. Aside from yours, every tank older than 10 years had a diversity ≤ 155.

These results suggest that your efforts to replenish diversity have made a big difference. Your diversity is almost double that of other >10 year old tanks.

Next the balance. Balance scores tell you how similar your sample was to other reef tanks. It probably won't surprise you to learn that your microbiome is quite different from others'. A score of 1 would mean your microbiome was identical to the average... your score (0.12) means that the major families of microbes found in aquariums are present at very different levels in your tank than in the average tank.

This doesnt mean your microbiome is unhealthy. It means its very different from the average. Considering the health of your tank and the differences in your reef keeping practices, I see no reason to consider this profile a problem. On the other hand, if there is something about your tank's behavior that consistently differs from others, this could provide a clue as to why.

You can see the basis for this score in part 2. Your tank has an unusually high level of Helicobacteraceae (the big red chunk in part 2), which is normally a very small fraction of the community. You may recognize the name from the bacterium that causes ulcers and other GI diseases in humans (Helicobacter pylori). Many members of this family are associated with animal surfaces, colonizing the GI tracts of various animals. Other members are associated with deep sea sediments and other sulfide rich environments.

That has me thinking... I believe you use an reverse under gravel filter, is that right? I would love to test the sediments from your filter and see if Helicobacteraceae are especially abundant there. I speculate that the high levels of Helicobacteraceae may result from this filtering method.

(again, no reason to consider this a problem. Its a big difference, and I'd like to understand differences like this)

Your tank is also very low in the families that typically make up a large fraction of the community, including Pelagibacteraceae and Flavobacteriaceae. These are often the most abundant types in natural ocean water samples, and also in aquariums. You have these groups, just at lower levels than is typical.

In the oceans, the relative levels of different heterotrophic bacteria are mostly driven by the kind of DOC available. I suspect the same is true in our tanks. Both of these groups have particular nutritional requirements that may be different from conditions in your tank. Flavobacteriaceae is specialized for taking up polysaccharides and proteins. Pelagibacteraceae is specialized for life in low-nutrient waters, and needs reduced sulfur compounds like DMSP as well as glycine for growth.

I suspect these differences result from the balance of nutrient important and export in your system. I know you've long been an advocate of natural foods. I'd love to hear more about your feeding practices to think about how this may be affecting the microbial community.

Like a surprising fraction of tanks, yours was relatively low on nutrient processing microbes. I want to be clear this wasnt universal, its not that we can't detect them. Some tanks just have bigger populations than others, we've seen this over and over now.

This doesnt mean they are absent in yours, of course, it means the populations are relatively small. I would like to explore this further. I suspect that some tanks rely more on other export processes, leading to lower populations of ammonia-oxidizing or nitrite oxiding microbes. I also suspect bioload and feeding play a role. I'd love to hear more about your bioload, feeding practices, and whether you have any macro algae (e.g. a refugium) in your system.

(Sorry for all the questions, as you recall we had some technical issues getting these details logged on the sample registration page)

You tank was completely free of known bacterial fish pathogens and known bacterial coral pathogens. I need to emphasize this does not address eukaryotic parasites like those that cause Ich; just the prokaryotic pathogens (Bacteria or Archaea). Still, given your advocacy of a no QT approach, this is a noteworthy finding. While 1 out of 8 tanks had a known fish pathogen (Photobacterium damselae), and 1 out of 10 tanks in my first batch had a known coral pathogen (Aquarickettsia rohweri), yours had no evidence of any known pathogens.

--


I suspect this is long enough and will stop there for now, but I'll be curious to continue discussing your interesting sample. Thanks again for participating!
 

AquaBiomics

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Does the multi decade health and production from Pauls system have any weight compared to the measure that a microbial species is lacking

If those species deemed lacking are boosted, what will be the impact in the tank claimed, how can the measures be put to use or aid recourse—-what is actually wrong with the tank given the measure? Would we think anything is wrong with the tank other than the bac testing
Hi Brandon,

I'm afraid I dont understand your question, could you clarify? Sorry, maybe its just too early in the morning and no enough coffee yet.

[edit I'm gonna leave the "no enough coffee yet" typo cause I think it perfectly captures the feeling of not enough coffee! :) ]
 
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sixty_reefer

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Hi Paul,

Here are my thoughts on the microbiome of your famous aquarium, the most mature reef tank I've yet had the privilege of testing. Both your water and biofilm samples contained plenty of DNA so these conclusions are based on analysis of thousands of high quality DNA sequences from your sample.

First the diversity (which is simply the number of different kinds of microbes found in your sample). Your tank was more diverse than 2/3 of those I sampled. This is even more impressive when you consider its age. Older tanks tend to have lower diversity ... tanks <5 years old ranged from about 100 to over 600. Aside from yours, every tank older than 10 years had a diversity ≤ 155.

These results suggest that your efforts to replenish diversity have made a big difference. Your diversity is almost double that of other >10 year old tanks.

Next the balance. Balance scores tell you how similar your sample was to other reef tanks. It probably won't surprise you to learn that your microbiome is quite different from others'. A score of 1 would mean your microbiome was identical to the average... your score (0.12) means that the major families of microbes found in aquariums are present at very different levels in your tank than in the average tank.

This doesnt mean your microbiome is unhealthy. It means its very different from the average. Considering the health of your tank and the differences in your reef keeping practices, I see no reason to consider this profile a problem. On the other hand, if there is something about your tank's behavior that consistently differs from others, this could provide a clue as to why.

You can see the basis for this score in part 2. Your tank has an unusually high level of Helicobacteraceae (the big red chunk in part 2), which is normally a very small fraction of the community. You may recognize the name from the bacterium that causes ulcers and other GI diseases in humans (Helicobacter pylori). Many members of this family are associated with animal surfaces, colonizing the GI tracts of various animals. Other members are associated with deep sea sediments and other sulfide rich environments.

That has me thinking... I believe you use an reverse under gravel filter, is that right? I would love to test the sediments from your filter and see if Helicobacteraceae are especially abundant there. I speculate that the high levels of Helicobacteraceae may result from this filtering method.

(again, no reason to consider this a problem. Its a big difference, and I'd like to understand differences like this)

Your tank is also very low in the families that typically make up a large fraction of the community, including Pelagibacteraceae and Flavobacteriaceae. These are often the most abundant types in natural ocean water samples, and also in aquariums. You have these groups, just at lower levels than is typical.

In the oceans, the relative levels of different heterotrophic bacteria are mostly driven by the kind of DOC available. I suspect the same is true in our tanks. Both of these groups have particular nutritional requirements that may be different from conditions in your tank. Flavobacteriaceae is specialized for taking up polysaccharides and proteins. Pelagibacteraceae is specialized for life in low-nutrient waters, and needs reduced sulfur compounds like DMSP as well as glycine for growth.

I suspect these differences result from the balance of nutrient important and export in your system. I know you've long been an advocate of natural foods. I'd love to hear more about your feeding practices to think about how this may be affecting the microbial community.

Like a surprising fraction of tanks, yours was relatively low on nutrient processing microbes. I want to be clear this wasnt universal, its not that we can't detect them. Some tanks just have bigger populations than others, we've seen this over and over now.

This doesnt mean they are absent in yours, of course, it means the populations are relatively small. I would like to explore this further. I suspect that some tanks rely more on other export processes, leading to lower populations of ammonia-oxidizing or nitrite oxiding microbes. I also suspect bioload and feeding play a role. I'd love to hear more about your bioload, feeding practices, and whether you have any macro algae (e.g. a refugium) in your system.

(Sorry for all the questions, as you recall we had some technical issues getting these details logged on the sample registration page)

You tank was completely free of known bacterial fish pathogens and known bacterial coral pathogens. I need to emphasize this does not address eukaryotic parasites like those that cause Ich; just the prokaryotic pathogens (Bacteria or Archaea). Still, given your advocacy of a no QT approach, this is a noteworthy finding. While 1 out of 8 tanks had a known fish pathogen (Photobacterium damselae), and 1 out of 10 tanks in my first batch had a known coral pathogen (Aquarickettsia rohweri), yours had no evidence of any known pathogens.

--


I suspect this is long enough and will stop there for now, but I'll be curious to continue discussing your interesting sample. Thanks again for participating!

@AquaBiomics your work surprises me every day thank you for the service you provide in taking this great hobby forward, you are doing an amazing job helping us understanding this hobby further than just water analysis. Could I ask you a small question regarding the work you do. I have noticed that you mentioned that Paul’s tank has double of the microbe for a tank of its age compared to others of similar age and some younger tanks have more microbe diversity from the test shown. Could the microbe diversity in a tank be connected to how we introduce bacteria, I believe paul still adds fragments often to his tank bringing new diversity every time he does so. Compared to other older tanks that are fully stocked and less things get added. Younger tanks will have more microbe diversity as in average more fragments are added on the first few years.
I think what am trying to ask is, could bacteria diversity be improved in older tanks by introducing small fragments of live rock to reseed the tank with microbes that were once lost. If the OP were to add a few pieces of live rock to his tank would we be seeing a New higher score in is test a few months from now?
 

AquaBiomics

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@AquaBiomics your work surprises me every day thank you for the service you provide in taking this great hobby forward, you are doing an amazing job helping us understanding this hobby further than just water analysis. Could I ask you a small question regarding the work you do. I have noticed that you mentioned that Paul’s tank has double of the microbe for a tank of its age compared to others of similar age and some younger tanks have more microbe diversity from the test shown. Could the microbe diversity in a tank be connected to how we introduce bacteria, I believe paul still adds fragments often to his tank bringing new diversity every time he does so. Compared to other older tanks that are fully stocked and less things get added. Younger tanks will have more microbe diversity as in average more fragments are added on the first few years.
I think what am trying to ask is, could bacteria diversity be improved in older tanks by introducing small fragments of live rock to reseed the tank with microbes that were once lost. If the OP were to add a few pieces of live rock to his tank would we be seeing a New higher score in is test a few months from now?
An interesting question that we've been discussing a lot recently.

I've heard good arguments for why we should expect decreasing diversity in a tank with age. Over time extinctions accumulate, and aren't replaced by new immigration. Like what happens on a remote island far from any other landmass.

On the other hand, many of our tanks don't really fit the "no immigration" part of the model. Many of us add things all the time, even if the tank is relatively old. If you add new livestock regularly for years, this would seem to favor increasing diversity with time.

During the early stages of establishing a tank, it is clear that diversity can rapidly increase. See this figure from my study of dry rock vs live rock in new aquariums
diversity-over-time.jpg


But the trend is over time for tanks to converge on a relatively low diversity state (~150 types). I need to emphasize that we have so few old tanks in the database, this trend is *not* statistically significant and may be just a quirk of the few old tanks we've sampled. I'm adding to this in the next round.

Paul's is the outlier in that regard, with a 47 year old tank that has a diversity equal to the average tank <5 years old.

Several members of my local club and I are thinking about adding some new high quality live rock to our tanks to see if we can increase diversity this way, and see what effects those changes have.

I will end by saying I think its important to remain agnostic at this point about the benefits of diversity. Its clear that diversity promotes productive and resilient ecosystems in nature. But the specific levels of diversity that are best for an aquarium, and the specific benefits of that diversity, remain to be explored.

I think most of us can agree that some level of diversity is beneficial but I don't think anyone can claim at this stage to know what is the "best" level of diversity for a healthy aquarium ecosystem. So at this stage, I think it makes sense to evaluate these numbers relative to other tanks, evaluating tanks as "high diversity" or "low diversity" rather than "good diversity" or "bad diversity". Like Alkalinity, Nitrates, or Mg, I imagine there will be a wide range of views on what levels are best.
 

Randy Holmes-Farley

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I would just add to what has been said that, in my opinion, it is not yet possible to characterize these sorts of analyses as good or bad. I would give a contorted analogy to a painting. A detailed scientific analysis of all of the colors and shades tells you what comprises the painting. It doesn’t tell you if it is a good piece of art or if you will enjoy looking at it, except perhaps in the most extreme cases.
 

lexinverts

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AquaBiomics tested my water a few weeks ago and I am all excited to know what it means as I can't interpret most of it so I need Randy who has more degrees than a thermometer, and I am an electrician with a fish tank.

Years ago I couldn't spell Lectrician but now I are one.

Thanks for sharing your results, Paul!

Your system could be a really important data point as we learn more about reef tank microbial ecology. I am especially interested to see if we can learn more about how your husbandry practices, such as frequently adding water and rock from Long Island Sound, have influenced your tank's microbiome.
 

AquaBiomics

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I would just add to what has been said that, in my opinion, it is not yet possible to characterize these sorts of analyses as good or bad. I would give a contorted analogy to a painting. A detailed scientific analysis of all of the colors and shades tells you what comprises the painting. It doesn’t tell you if it is a good piece of art or if you will enjoy looking at it, except perhaps in the most extreme cases.
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,
Tolstoy said:
All happy families look alike; each unhappy family is unhappy in its own way

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.
pcoa-w-circles.jpg


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.
 
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Paul B

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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.

 

brandon429

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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.
 
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Paul B

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The other thought is how polluted is the Sound? And were is the closest outflow from a sewage treatment plant?

I don't think it is very polluted where I collect because I am about 80 miles from the City and the Sound is 22 miles across here to Connecticut so it is basically the Atlantic Ocean.
 

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AquaBiomics tested my water a few weeks ago and I am all excited to know what it means as I can't interpret most of it so I need Randy who has more degrees than a thermometer, and I am an electrician with a fish tank.

Years ago I couldn't spell Lectrician but now I are one.
Well you biodiversity is a lot different than a typical mature reef. Maybe you should tell them your the gold standard mature reef tank.
 

AquaBiomics

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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 is a beautiful sponge! I have a similar one (although nowhere near as big) that was sold as Collospongia sp. but I know little about sponge ID. Wonder if we have a sponge expert on the forum?

Sponges are filter feeding machines, and they specialize in small particles including bacteria. See for one example this study of filter feeding in Caribbean sponges. With such a large biomass of sponge in the tank I bet it is affecting the microbial community. Interesting! My survey form includes sponges, I will have to look into whether the presence of sponges is related to abundance of any microbial families.

One of the families present at low levels in your sample is Pelagibacteraceae, which are free-living bacteria that actively swim around in the water. It would make sense that active filter feeding would reduce those relative to other microbes that primarily live attached to surfaces. On the other hand Flavobacteriaceae are also low in your sample relative to the typical profile, and these are mostly surface associated.

I looked a little deeper into the high abundance of Helicobacteraceae in your sample. Curiouser and curiouser... its all a single type, not detected in any other sample. This matches a bacterium that's been previously found in environmental samples but hasn't been identified beyond the Family level, so I can't say whether its one of those associated with animal guts or sulfidic sediments.
But its interesting to explore. This sequence is a perfect match to a bug found in many other studies, so we can look at where its been found. Mostly aquatic environments, including lots of estuaries and sediments.
Theyre found worldwide including pretty close to you (I don't see records for the LI sound itselt but pretty close!)
 
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