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

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AquaBiomics

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Thanks, I'd looked at that table when I sent the samples in but didn't remember this. So they require glycine and DOC?
That's very interesting! And interesting that glycine is not one of the amino acids in Fuel.
I wonder which of the available amino acid supplements contain glycine specifically?
Fuel is the only one I have at the moment, and I don't see specific ingredients for other products online.
Lots of folks swear by AcroPower; perhaps it contains glycine? And what about Reef Energy?

It would be interesting to see if carbon dosing with the addition of glycine supplement increases pelagiobacteria.

Another way of addressing this question is this -
Based on your data, what supplement products are those with sizable pelagiobacteria concentrations using?
I know that at least one client with multiple tanks was dosing Vodka and has more Pelagibacteraceae levels. So maybe it doesnt take any special product, just some source of DOC. I'll dig into this tonight and see if there are any significant relationships in the DB yet for carbon sources.

I should also clarify that the information about nutritional requirements is not based on aquarium studies. This group requires glycine, but that doesnt mean glycine is limiting for their growth in aquaria. Depending what a person feeds the tank, I think many of our tanks are getting a big dose of mixed amino acids every day from the food itself.

With that said, I'm setting up some nutrient dosing experiments in the lab today to test some of these ideas.
 
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AquaBiomics

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Most nitrifying bacteria are 'motile' - they can go to wherever the food source is the greatest. It was once thought that they just sat in one place - that is not the case. More interesting is that there are many more bacteria that are nitrifying than the ones we commonly 'desire'
Are you referring to gliding motility or actual free-swimming pelagic forms? I admit, I've been kind of lumping both non motile and gliding types together as "not free living". The only really free-swimming nitrifiers coming to mind for me are in the Cenarchaeaceae, but perhaps you know of some others?

I like your point about diversity in nitrifying microbes. Even whats been shown from the reports doesn't really do this justice because I've lumped the types together at family or genus levels. I'll do a more detailed analysis soon to describe the full diversity of nitrifying microbes in aquariums.
 

AquaBiomics

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They may be commonplace but do we know what they do, and there importance to the reef zones? and are they necessary enough for there low levels in our tanks to be of initial concern?
Necessary, no, I think the variation among our tanks makes it hard to argue that any particular type or level is really necessary. Certainly quite a few tanks that support healthy fish and corals have low levels of Pelagibacteraceae.

The specific metabolic activities of this group remain an area of active study. But I think theres a meaningful answer to your question that doesnt depend on ongoing research. Pelagibacteraceae are abundant heterotrophic bacteria, so one thing we know they do is compete with other microbes for nutrients. The microbial soup is a constant tug of war for dissolved nutrients. Without the Pelagibacteraceae, someone else is getting more nutrients than they would if there were a lot of Pelagibacteraceae present, like in the ocean, and like in other tanks.

Someone's getting the nutrients, and blooming instead of Pelagibacteraceae. In my tanks, thats Alteromonadaceae. In other tanks, I've seen others bloom. So the question may not just be how does Pelagibacteraceae help the tank (if it does at all), but rather how does the group that blooms in its place affect the tank?

I still don't have the specific answer, but my point is that one of the important ways a microbe can benefit the community is by keeping others in check through competition for resources.
 

lexinverts

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MnFish1

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Great article, Eli!

Curious - what do you base this on - was it well written - well researched or some other reason? Don't take this as a snarky response - because I dont mean it that way
 

lexinverts

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Curious - what do you base this on - was it well written - well researched or some other reason? Don't take this as a snarky response - because I dont mean it that way
I reviewed an early draft, so I know it is well written. I observed some of the experiments in his lab, and I also know him to be a well regarded scientist, so I know it is high quality work. I also have already used some of the recommendations that have come from this work in my own reef tanks. Does that help?
 

MnFish1

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I reviewed an early draft, so I know it is well written. I observed some of the experiments in his lab, and I also know him to be a well regarded scientist, so I know it is high quality work. I also have already used some of the recommendations that have come from this work in my own reef tanks. Does that help?
Sorry I wasn't clear - I meant - on what do you base your conclusion this it is a great article? With useful information. where was it published? Peer reviewed? Again - I''m not being snarky here - I'm not sure where the link is taking me or where its from.
 

sixty_reefer

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Sorry I wasn't clear - I meant - on what do you base your conclusion this it is a great article? With useful information. where was it published? Peer reviewed? Again - I''m not being snarky here - I'm not sure where the link is taking me or where its from.
Is a peer review really needed in the hobby regarding bacteria, I find the article interesting, I also find most BRS investigates interesting and informative. Do we really need a peer review on BRS also?
 

lexinverts

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Sorry I wasn't clear - I meant - on what do you base your conclusion this it is a great article? With useful information. where was it published? Peer reviewed? Again - I''m not being snarky here - I'm not sure where the link is taking me or where its from.
You previously asked me if I was basing my conclusion that it was a great article on whether it was well written and well researched, and I said yes. Now you seem to be asking a different question. I also found it useful, because I have some live rock determined to be high quality by AquaBiomics, and I have moved some to a tank that scored low for diversity and is struggling. We'll see if it makes a difference next time I get my tanks tested.

My link goes to a Reef2Reef article just posted by AquaBiomics.

If you would like to read his peer-reviewed articles, you can go here.
 
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MnFish1

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You previously asked me if I was basing my conclusion that it was a great article on whether it was well written and well researched, and I said yes. Now you seem to be asking a different question. I also found it useful, because I have some live rock determined to be high quality by AquaBiomics, and I have moved some to a tank that scored low for diversity and is struggling. We'll see if it makes a difference next time I get my tanks tested.

My link goes to a Reef2Reef article just posted by AquaBiomics.

If you would like to read his peer-reviewed articles, you can go here.
Thanks alot - always interested. Appreciate your reply. I guess I wonder 'how did aquabiotics determine it to be 'high quality' - otherwise - all good
 

PSXerholic

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Ok, so I decided to join this thread and perform a few tests for my own interest.

Many know me from the R2R forum and also as the guy who came up with the Witchhazel tank treatment against RTN/STN while resolving the intitial culprit leading to TN issues.

Tank is doing great so far, apart from "There is always something" .

My interest will be focused on the bacterial diversity as of now, and then in soon future, a test before and after a 12 day Witchhazel Treatment since this test may likely bring in some results and evidence on the impact of Witchhazel on the biology in the tank ;-)

Very exited to do this!
Thanks to everyone who shared their results so far in this thread.

-Andre
 

AquaBiomics

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Ok, so I decided to join this thread and perform a few tests for my own interest.

Many know me from the R2R forum and also as the guy who came up with the Witchhazel tank treatment against RTN/STN while resolving the intitial culprit leading to TN issues.

Tank is doing great so far, apart from "There is always something" .

My interest will be focused on the bacterial diversity as of now, and then in soon future, a test before and after a 12 day Witchhazel Treatment since this test may likely bring in some results and evidence on the impact of Witchhazel on the biology in the tank ;-)

Very exited to do this!
Thanks to everyone who shared their results so far in this thread.

-Andre
Hi Andre, that's a stunning tank and I can't wait to see its microbial community.

I will be really curious to see how the witchhazel treatment affects the microbiome. Its exactly the kind of experiment I was hoping this technology would enable, so I'm really glad you posted this. When it comes time for that experiment, if you're interested, I'll throw in some extra supplies so you can also sample the coral mucus of treated / untreated corals. It'd be nice to measure that too, since the coral mucus microbiome is different from the surrounding seawater but the medication may have important effects there (that may or may not be different than its effects on water community)
 

PSXerholic

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Hi Andre, that's a stunning tank and I can't wait to see its microbial community.

I will be really curious to see how the witchhazel treatment affects the microbiome. Its exactly the kind of experiment I was hoping this technology would enable, so I'm really glad you posted this. When it comes time for that experiment, if you're interested, I'll throw in some extra supplies so you can also sample the coral mucus of treated / untreated corals. It'd be nice to measure that too, since the coral mucus microbiome is different from the surrounding seawater but the medication may have important effects there (that may or may not be different than its effects on water community)
Thank you Sir ;-)
Tank is now running in the 2nd year with the application of a very strict Trace element dosing regime. I do refresh usually the tank biweekly with some Biodigest but recently that seemed not being helpful against some very resistant Cyano species which under the microscope, gave me hard time to reduce it with anything I know that normally helps against it. Hence I believe the current biodiversity isn't that good, will see soon :)

Your'e absolutely right concerning the Coral mucus symbiotic bacteria biology, which is indeed very different from the surrounding bacteria in the water, attacking the Mucus layer when the Coral is weakened and it's own bacteria can't produce sufficiently antibacterial agents and antibiotics to defeat the pathogens in the water.
I have done some very nice Microscopic Video and observations in the beginning of this year where I could observe and see the tissue impact, in order to see upcoming RTN on a Coral without damaging it.
This link is a publication I shared a lot which explains this theories in more detail.

If you want to go right to the point, read page 16 or Chapter 1.4.4 at least.
However, the entire article provides a very interesting summary of the Coral Tissue and it’s functions as far it’s explored for now……
Simply click the PDF download button.

So back to the tests, (un)fortunately I do not experience any TN issues anymore, hence it will be difficult to test coral mucus or tissue, but if you like I can send that too at least from healthy corals, knock on wood, lol.

I'm interested in the bacteria diversity in the water especially prior and after a Witchhazel treatment, simply to see how and which bacteria is affected by the treatment. I can also extract Mucus from corals prior and after, good point.
I have gotten feedback that in multiple cases specific Cyano species went away, but I'm unsure if that is a result of the Witchhazel's antibacterial tannins or due to a rebalancing of the biology! Withchazel is known for antibacterial characteristics, but never could find any public publications where it is explained what the Witchhazel really does, and there is so much room for guesswork. All I found was that it is antibacterial to many pathogens but limited to probiotics.

Here some Videos:

Green Inked/Dye Coral surface - This particular species populated during RTN inside the Mucus layer, not a coral Nemacotyst!

Growing Cyano:

Zoox intruded by microorganisms
 

rushbattle

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I don't know where else to post this, but I would like to thank @AquaBiomics for his free advice so far! I put a small piece of real live rock from my rock bin into my tank that was suffering from cyanobacteria overrun, and it has slowly reduced the cyano issue over a few weeks! The corals have larger growth margins, and better polyp extension as well. Correlation is not causation, but I will certainly be using this service in the future to figure out what is going on, thanks Eli!
 
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Huskymaniac

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Very intrigued. I actually caught a myco infection from my tank at the beginning of the year and all of my fish are asymptomatic. I ended up setting up a new tank in case my Myco tank crashed etc. I added a huge pentair uv sterilizer and am pretty curious if it will show up on the test.
 

AquaBiomics

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Very intrigued. I actually caught a myco infection from my tank at the beginning of the year and all of my fish are asymptomatic. I ended up setting up a new tank in case my Myco tank crashed etc. I added a huge pentair uv sterilizer and am pretty curious if it will show up on the test.
That will be interesting! Hope you're doing well, I know my colleague who had an M. marinum infection from a cut on her hand was frustrated how long it took to heal. This bug hasnt shown up yet on the tests yet but that's consistent with the relative rarity of these infections among reef keepers. If it is there, we will find it...
 

Huskymaniac

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That will be interesting! Hope you're doing well, I know my colleague who had an M. marinum infection from a cut on her hand was frustrated how long it took to heal. This bug hasnt shown up yet on the tests yet but that's consistent with the relative rarity of these infections among reef keepers. If it is there, we will find it...
I just put in my order and will definitly let you know which one is the myco tank. Ordered 1 for my new tank that has a Dino problem also. I cut my hand on the overflow and you know the rest. I am doing well though. Infection was cleared in about 2 months but stayed on antibiotics for the full 6. I have been super hesitant transfering frags to the new tank as I didnt want to contaminate the new tank. Cant wait to see what it shows. Can mycobacterium actually be outcompeted and eliminated from a tank?
 
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