Bacterial fish pathogens in the reef tank

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The fish that were in that system were two Clowns and a Coral beauty both of which I've had for 2+ years with no recent fish additions which makes the presence all the more interesting. They've since been moved to a QT with a small Hippo and Gem tang (coming up on 30 days of observation and 14 days of therapeutic copper with no ill signs). I do eventually want to keep Anthias (which I believe are some of the more susceptible fish to P. damselae) in my main display so treating prophylactically with baths is likely the path I'm going to take with these fish.

For the old display, I'm tempted to do an experiment of a few major water changes (that tank is actually fish-less right now) and potentially try the low dose Cipro treatment @AquaBiomics discussed when dealing with BJD. If I go that route, is there a period of time I should wait to run another biome test (or two) so that there is higher confidence in the results actually reflecting the reality in the tank? I assume that it being free-living, major water changes and even a light antibiotic dose would nock some of the numbers (and thus chance of a DNA sample hit) pretty drastically to start, but there might still be low-levels in the tank which would need to build back up (to increase the likelihood of detection). Based on that plan, would you recommend another test immediately after treatment and then another in a couple months (assuming I keep the tank up a running)?
 
It can be as fast as a little over two weeks or as long as a little over a month. It depends on when they receive your sample relative to when they send in a batch for sequencing. Take a look at their sampling schedule here:


For the next batch, if they receive your samples by April 30th, you should expect to see your results 2 weeks later. I am waiting to test my tank until next week, and then I will give it to Eli around the 28th or 29th, which will result in me experiencing the minimum turn around time.
Thanks I was looking for that page and couldn’t locate it. Guess it should be any day as I am in this group.
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AquaBiomics

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Sorry for the delay - half the reports have gone out, half the data are hung up at the sequencing facility. Very frustrating weekend waiting for them to get back to work. I expect to get the remaining data for this batch any minute, and process data & send reports for the rest of the day.
 

JCTReefer

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I received my report this morning. Speaking of bacterial, I had a pretty high number of Vibrio Fortis. I’m guessing a contributing factor is my lack of maintenance over the last year. Very few water changes due to dino issues. From all the exhausting reading I had done on various types of dinos, it seemed water changes were a bad thing when battling dinos. And by doing them I was adding fuel to the fire dinos wise. I’m wondering if my lack of maintenance is the cause for such high numbers. I also lost my Yellow Tang a few months back to a bacterial issue and likely something else. The Edna test showed no parasitic infestations though. I’m still puzzled on the reason for its death. I’m going to try and address the Vibrio by upping my
maintenance routine. I’m not sure if this is the only approach, but it’s the plan. Then I’ll have another test done in a few months. The balance of microbial groups in my tank was terrible also. The thing is, all this livestock at some point will go in the new DT. I’m not sure if there’s anything that needs to be done to this tank before that can happen. The main thing I was concerned about was fish pathogens being transferred to the new DT. But now the Vibrio has me concerned. That, and I’m wondering if I should use any of this rock in the new tank. I was finally able to buy some Reef rubble today from Aquabiomics. Finally scored some!!!! You gotta be quick on the draw. This will go in the new tank to start seeding. Here is a snapshot of my numbers. Very interesting stuff!!! I don’t know how these numbers compare to other tanks, but seem high compared to a typical sample. Of course in my sample there’s not much on the table, so I guess something has to fill the graph.

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If one wanted to use this test to help assure that no pathogens had been introduced into a QT system, how long would that system need to run to ensure reasonable accuracy? I'm asking because since I have a known pathogen in one system, but want to try treating it in a separate holding/QT tank, but I'm curious how long it'd need to run there to feel confident that the pathogen is no longer present.

Along the same lines, how long after a recent addition to a QT tank would pathogens take to turn up in the test? For example, if I bring in a batch of live rock (or coral over time) how long should I wait until I take a sample from that tank?
 

JCTReefer

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If one wanted to use this test to help assure that no pathogens had been introduced into a QT system, how long would that system need to run to ensure reasonable accuracy? I'm asking because since I have a known pathogen in one system, but want to try treating it in a separate holding/QT tank, but I'm curious how long it'd need to run there to feel confident that the pathogen is no longer present.

Along the same lines, how long after a recent addition to a QT tank would pathogens take to turn up in the test? For example, if I bring in a batch of live rock (or coral over time) how long should I wait until I take a sample from that tank?
That’s an interesting question. When I sent my sample in, I had a single fish that had been in quarantine for about 2 months. No medications used. I’d be curious to know the answer. Here’s a screenshot from my Edna report. Or at least the fish pathogens part. Pretty interesting. I would think 2 months would be long enough for something to show up, but who knows. Even though no parasites were found, I’m still going to use the Hybrid TTM before this fish goes in my DT.

 

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If one wanted to use this test to help assure that no pathogens had been introduced into a QT system, how long would that system need to run to ensure reasonable accuracy? I'm asking because since I have a known pathogen in one system, but want to try treating it in a separate holding/QT tank, but I'm curious how long it'd need to run there to feel confident that the pathogen is no longer present.

Along the same lines, how long after a recent addition to a QT tank would pathogens take to turn up in the test? For example, if I bring in a batch of live rock (or coral over time) how long should I wait until I take a sample from that tank?
Great idea. I think they would show up almost immediately.

I also think that the eDNA test would be quite sensitive to parasites in a QT tank. The eukaryotic and bacterial diversity should be quite low in a QT tank, so if there were any parasites present, their DNA should show up in the test as a strong signal. When the eDNA tests might not detect something (that is actually there) is when there is lots of DNA in the water from a high diversity of organisms and it swamps out the weaker DNA signals.
 
Great idea. I think they would show up almost immediately.

I also think that the eDNA test would be quite sensitive to parasites in a QT tank. The eukaryotic and bacterial diversity should be quite low in a QT tank, so if there were any parasites present, their DNA should show up in the test as a strong signal. When the eDNA tests might not detect something (that is actually there) is when there is lots of DNA in the water from a high diversity of organisms and it swamps out the weaker DNA signals.
I'd love to hear from @AquaBiomics on the general sensitivity of the eDNA test. The main thing I wasn't sure about was if something effectively had to reach a certain population size (either active or historical) to have a decent probability of actually being collected in the sample. For bacterial pathogens, I could imagine that a sizeable enough of a population would build up over a couple weeks/months, but with protozoans (like Ich) while have longer life cycles I wasn't so sure. I realize there isn't a 100% answer to this, but again I'm curious if it turns out to be a valid use of the test (for those that might be willing to say test a given "batch" of things say monthly).

Basically I'm just not sure how much DNA is floating around in a tank when dealing with a relatively small tank and time window of something relatively new (and likely in low populations to start).
 

AquaBiomics

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I'd love to hear from @AquaBiomics on the general sensitivity of the eDNA test.
This is the million dollar question. Or some number of dollars anyway.

One answer, the boring and safe answer, is that more studies are needed. The key detail here is what fraction of the eDNA sample does the organism of interest contribute? Really the only way to be sure is with controlled experiments, and I continue to have a difficult time getting my hands on predictably sick fish for experiments. Plus, the usual challenge that there appear to be not enough hours in the day by a factor of 4 or so lately.

With that said, in this time sampling tanks, I've seen a few things that lead me to believe the eDNA test is pretty sensitive for pathogens.

For example, about 10% of the batches of live rock I've bought have had pathogens or parasites. (Obviously I didnt sell those! :) ) This is rock in a recently sterilized tank with new water. There cant be that much biological material there... no infected fish, for sure.

And I routinely find eDNA from interesting, sample-specific contaminants that I know cannot exist as a large biomass in the tank, like terrestrial plants. Again, this leads me to suspect its pretty sensitive.

I appreciate thats not a very quantitative answer, but its what I have at the moment. I'm currently testing a couple things in the lab process to improve the sensitivity in principle.

And experimental tests of the sensitive are high on my list. In my mind the gold standard will be, if we introduce a sick fish in a clean tank how quickly can we reliably detect its presence?
 
For example, about 10% of the batches of live rock I've bought have had pathogens or parasites. (Obviously I didnt sell those! :) ) This is rock in a recently sterilized tank with new water. There cant be that much biological material there... no infected fish, for sure.
This is actually pretty helpful even if not that quantitative. How long after introducing the batch of live rock did you test? Do you ever re-test a negative batch, say a month later, to see if you got any false negatives?

I'm going to take a sample from my QT'd tank that had a piece of live rock from the infected tank and see what those results are. If they come back positive, I'd be happy to send to a piece of that rock if you wanted to use it as "seeds" for any experiments on your end.
 

JCTReefer

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My excitement levels went through the roof after finding out pathogens could be detected using DNA sequencing!! My whole reasoning for having my QT sampled was strictly for the eDNA test. That, and I didn't want to treat prophylactically if it wasn't necessary. Given the response below, I think ill have it retested. That is after I run this fish through treatment. I'm curious to know if the results will be different. What probability do give that the tank is pathogen free? Don't worry, I'm not holding anyone to anything. With the time it takes to have samples processed, this won't be an option for me on every batch of fish. I did figure out the time window thing, which will greatly increase the processing speed. I just sent my samples in at the worst possible time that took the longest to get results. I'll have the "new" 210 DT tested after all livestock are introduced. That and have the old 54 tested again also. I could have prepared the samples wrong and that's what caused the unusual pattern. Doubt it.. I watched the video several times and read the directions thoroughly!! 🤣 Now this response below was above and beyond anything I would ever expect from a company. Two thumbs up there.. And this was just a portion of it.

"Now for the eDNA test. This found no evidence of any parasites or pathogens in either tank. I should emphasize, however, that both tanks showed an unusual pattern that would reduce our sensitivity to detect parasites. In the 54g, the great majority of DNA in the sample came from a specific sponge. This sponge is very common in reef tanks and is not a problem at all, whats unusual is to have it account for >90% of the DNA. The 20L also showed a DNA profile dominated by just a couple types. In this case, an unclassified phytoplankton species in the Ochromonadales makes up about 1/3 of the sample, and another unclassified phytoplankton species makes up about 60%.

I'm not concerned about either the phytoplankton or the sponge, just that they consumed a lot of the sequencing coverage so the sensitivity for detecting anything else was lower than usual. It would be great to retest these tanks for eDNA along with any future samples you may send, so we can compare."
 

FishGuy2013

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So I qt everything in my tank and run uv. All fish go through copper and prazi. I go my test back and I am at .00406 of photobacteriam damsalae. Is the a way to distinguish if this was from my biofilm vs water column. I do not have ich, velvet, and/or uronoma. All fish eat and show no signs of anything. Now for some reason my potters is only out at night. He grazes all morning before lights on. I do have 5 tangs in tank so they are the bosses and they left him know early on. Should I even worry. Do you think potters is affected by this pathogen?

thanks
Robert
 

Humblefish

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Generally speaking, I don’t really worry about harmful bacteria or viruses in an aquarium because a healthy fish’s immune system is adept at fighting those off. Of course, there are exceptions because of their virulence (e.g. Vibrio, Septicemia) but the “good news” is any fish with those is going to die in QT before reaching your DT.
 

FishGuy2013

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Generally speaking, I don’t really worry about harmful bacteria or viruses in an aquarium because a healthy fish’s immune system is adept at fighting those off. Of course, there are exceptions because of their virulence (e.g. Vibrio, Septicemia) but the “good news” is any fish with those is going to die in QT before reaching your DT.
So then since I have qted for the main stuff then do not worry about the bacteria that is there because fish are healthy and eating. I am relieved because I have went through a lot of work to qt every snail, fish, and coral.
 

TexAgReefer

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So then since I have qted for the main stuff then do not worry about the bacteria that is there because fish are healthy and eating. I am relieved because I have went through a lot of work to qt every snail, fish, and coral.
I’m in a similar boat. My aquabiomics test revealed Photobacterium damselae, but nothing else (thankfully). I have 33 fish in my DT so trying to pull them out to treat for it is simply not likely.
 
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