I had my water tested but need explanation

[AquaBiomics]

I'm in awe reading this thread. I was born and raised in Queens NY but never had a marine tank unt I emigrated to Perth Western Australia in 1983. I only ever used 100% NSW that is collected from the Indian Ocean which is filtered through >500 micron, allowing all but the largest plankton through. The water is routinely collected from a depth of ~ 20 feet which is approximately another 20 feet above the substrate. Importantly, the water is always collected well off shore by ~ 3 km (>1 mile) and well upstream of any known pullution sources - ie., sewage drains, chemical processing plants and coal powered electricity plants.

This part of my post is directed to @AquaBiomics:
I'd be very interested in getting a sample of my water analysed by you, however, would a sample sent to you from such a large distance away degrade, skewing the results? If not, how do I arrange a delivery to you?

So jealous you moved that close to the reefs! What an interesting sample your tank would be. I sent you a PM to discuss thoughts on the challenges of arranging international sample shipping.

 

[chefjpaul]

As this is one of the most intriguing, yet possibility significant revolutions our hobby, It's still in an evolutionary status.

Development and the education could be a revolution or a rebellion knowing our fellow reefers, yet, we still need to go to our sentiment that we all preach, but do not follow.

Patience.


Lets gather data, evaluate, and come to conclusions, as there will never be facts on life involving diversity in an "each" individual ecosystems nor the same for those individual results. We can, as this evolves, learn, evaluate and improve our each glass box by listening, and communicating without speculating.

I have theories of dry rock that is a contradiction of many, yet it's about technique, nor not?

Dino's / cyano etc. ... same... "life", bacteria, etc... this whole "balance" thing I never comprehend, as there is no such thing in life, It's an equilibrium.
We test, talk, debate, and seek minuscule concentrations of those we don't comprehend. Let's find out why first.

 

[Lasse]

@AquaBiomics - If you want world wide samples - put me on the list. My tank and @Paul B :s tank have probably the same DNA of thinking and management. Could be interesting to see if our microbial lives have the same DNA

I note the lack of both ammonium and nitrite oxidizers in his tank. Make me thinking - do you track any huge population of the bacteria responsible for anammox (bacteria from bacterial phylum Planctomycetes - see this article https://www.frontiersin.org/articles/10.3389/fmicb.2014.00399/full) in his tank

Sincerely Lasse

 

[AquaBiomics]

@AquaBiomics - If you want world wide samples - put me on the list. My tank and @Paul B :s tank have probably the same DNA of thinking and management. Could be interesting to see if our microbial lives have the same DNA

I note the lack of both ammonium and nitrite oxidizers in his tank. Make me thinking - do you track any huge population of the bacteria responsible for anammox (bacteria from bacterial phylum Planctomycetes - see this article https://www.frontiersin.org/articles/10.3389/fmicb.2014.00399/full) in his tank

Sincerely Lasse

Hi Lasse,

Interesting question! I must admit I had not looked for this group since none of the commonly discussed annamox genera ever showed up in the results. But your question prompted me to dig deeper and this has led to an interesting finding.

The phylum Planctomycetes are present in most tanks (88%) but make up a small fraction of each community (median = 1.7%). Paul's levels were very close to this. These include two genera (gemmata and planctomyces) and a large number of Planctomycetes not identified to the genus level. Most of Paul's were not identified to the genus level. None of the annamox genera listed in the paper you linked showed up. So far, nothing interesting, I was ready to put it away again.

But I noticed the unidentified Planctomycetes *are* identified to the family level -- as Pirellulaceae. Which is associated with corals and sponges, especially in the deep sea, and most importantly has ammonia-oxidizing activity. There is little written about this family. Its not even described in my edition of The Prokaryotes (apparently there has been revision of this phylum since it was written). But there are plenty of primary papers out there mentioning it.

The reason this is exciting: this family is present in 71% of samples. You may have helped solve part of the mystery of the missing nutrient processing bacteria -- these deserve to be counted toward that total. I will do some more reading and if I continue to find support for this, I will add this to the list and push updated reports to the clients.

Many thanks!

 

[Paul B]

Atoll added this but is having trouble logging on so i will add it for him:

"Extremely interesting. Paul uses a reverse flow under undergravel filter which means the gravel will have lots of detritus in it as the pump supplying water to the UG will be pumping detritus into it and most must get trapped there. I used reverse flow UG many years ago. After a few years when I had to break it down it was loaded with detritus. In my last couple of tanks I have used no prefiltration what so ever unless you call a skimmer such which to some extent it is. I wonder how much this build up of detritus actually aids the general health of Paul's tank."

 

[Lasse]

I use a reversed flow also and even pump skimmate down there in the start. 1.5 years later - I had to dig it out of other reasons - it was clear as it was when I put in the sand

Sincerely Lasse

 

[Scrubber_steve]

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.

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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!

Hi Eli; I would seriously like to see this test performed on @glennf's aquarium water, accompanied by your commentary. Perhaps you two could come to some agreement?

 

[Twitchy]

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.

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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".

Hold On, I think I have something in my junk pile for this! Ehhhh... Biology smells and tastes funny... I think It would make a far better CNC