Bacterial fish pathogens in the reef tank

[AquaBiomics]

Hi everyone,

I've been testing the microbiomes of saltwater aquariums for about a year now, and one interesting thing I've noticed is that a reasonable fraction of reef tanks have one or more known fish pathogens. But they're not everywhere. I'm starting this thread to share these data with you, and discuss the possibility that undiagnosed bacterial infections may contribute to fish diseases and mortality in our aquariums.


The bacterial pathogens I have seen so far:

Pathogen	Prevalence (% of tanks)	Abundance, % of community median (range)	Disease (reference)	Known Susceptible Fish
Photobacterium damselae	14%	0.19% (0 - 1.3%)	Photobacteriosis and similar infections (Rivas et al. 2013, Andreoni & Magnani 2014)	Damsel family, others?
Piscirickettsia salmonis	1%	0% (0 - 0.13%)	Piscirickettsiosis (Rozas & Enrique 2014)	Salmonids, others?
Vibrio fortis	57%	0.16% (0 - 19%)	Enteritis (Wang et al 2016)	Seahorses, others?

A few important caveats about these findings:

• Genetic Variation - there is a lot of variation within each bacterial species in terms of virulence. For example, in P. damselae there are different sub-species and types with known differences in virulence and host ranges. However, the marker used here can't resolve these beyond the species level. Still, since so many of the sub species and types in this group are pathogens for fish or humans, I feel comfortable listing it as a pathogen.
• Unknown Susceptibilities - these pathogens are typically discovered in aquaculture settings, where a single species is grown. As a result, the researchers don't immediately document the range of susceptible fish in the aquarium trade, so we lack this information for most of these pathogens.

In other words, based on what we do not know for sure -- its possible that the specific bacteria detected here are non-pathogenic, close relatives of the known pathogens. Or its possible that even if they are pathogens, the kinds of fish kept in that tank may not be susceptible. With that said, I think we all agree that unless we manage diseases, fish deaths are pretty common in the hobby. So it seems prudent to look into these pathogens as possible contributing factor.

One finding I'd like to highlight is the wide range of abundance we see for some of these. For example, consider Vibrio fortis. This bacterium is present in over half the tanks I've tested, but typically at very low levels (median = 0.16% of the community). However, in one tank it made up 19% of the community, more than 100-fold higher in relative abundance than the median level. It seems plausible that this extreme variation could play a role in the extent of disease caused by these bacteria.

Another important factor to consider is resistance. Taking P. damselae as an example, research has shown that fish can become more resistant to this pathogen with age, and some fish show genetic advantages in resistance. So it is possible that fish in the tank are not affected, even if their species generally is susceptible.

My questions for the community:
1. Have you experienced fish diseases or deaths that you believe were primarily caused by bacterial infections?
2. What are your practices for managing bacterial pathogens in your tanks?

Thanks for reading, I'll be curious to hear your thoughts.

 

[Lexinverts]

Yes, it is widely accepted that vibrios cause disease in seahorses. You’ve swabbed a few of my dead seahorsesbut I don’t think you found vibrios on them, did you?

We try to keep the water temperature between 70 and 72 in order to reduce the likelihood of vibrio infections. In my experience, it seems that keeping nitrate levels lower also helps keep seahorse vibrios in check.

 

[Susan]

I just lost one tonight (pretty sure) due to bacterial infection.

 

[Susan]

Do you run test on the fish that died and the water? After the analysis, do you give advice on what to do to correct any bacterial issues?

 

[Humblefish]

1. Have you experienced fish diseases or deaths that you believe were primarily caused by bacterial infections?

As we discussed over the phone, I would go months without seeing a virulent bacterial disease in my fish shipments. Even secondary infections from parasites/worms were rare. But then I would get in a "bad shipment" and experience primary bacterial diseases in a few of the QTs. (Not all of the fish were affected though.) Some of the "bad shipments" with bacterial diseases were due to fish being in the bags longer than expected due to shipping delays. And as a disclaimer, I did get into the practice of prophylactically dosing kanamycin once or twice during QT which probably helped offset infections as well.

2. What are your practices for managing bacterial pathogens in your tanks?

As a hobbyist, I almost never experienced bacterial infections in QT. However, every single fish got a 30 minute bath using Nitrofuracin Green Powder before entering QT. Nitrofuracin Green is a formulation of Nitrofurazone, Sulfathiazole Sodium, Methylene Blue and sodium chloride. @Dierks has been using it at double dose for 30 minutes to treat active infections with good success. Hopefully he chimes in with his experience.

 

[Dierks]

2. What are your practices for managing bacterial pathogens in your tanks?

Hey Guys, As Bobby mentioned I have been using NFG to try and figure out what works best with a few issues I have come across. I have so far treated several fish with bacterial infections and also treated fin rot with NFG double dosage baths for 30-35 minutes every day for 5-7 days. I have noticed that if I skip a day or two it isn't as effective if I do it every day. I also noticed my fish don't seem to mind the bath and none of them have reacted negatively to it. Of course every time I would walk in the room the fish that had the issues would hide as they knew what time it was!

I really like this combo of drugs and feel like it has been very beneficial when it comes to bacterial infections and happy I added it to my fish medical cabinet. I am also now leaning more on fenbendazole over Praziquantel, but that is for worms so it really doesn't apply to this conversation.

 

[AquaBiomics]

Yes, it is widely accepted that vibrios cause disease in seahorses. You’ve swabbed a few of my dead seahorsesbut I don’t think you found vibrios on them, did you?

We try to keep the water temperature between 70 and 72 in order to reduce the likelihood of vibrio infections. In my experience, it seems that keeping nitrate levels lower also helps keep seahorse vibrios in check.

I didnt include any of your seahorses in the last batch, I had so many paid client samples in that batch I had less room for the experimental stuff. I'll include them in a future run.

I do see that V. fortis has consistently showed up in your seahorse tank, and your RSM750. I didnt include it on the fish pathogen list initially so that may have gone unreported...

 

[AquaBiomics]

Do you run test on the fish that died and the water? After the analysis, do you give advice on what to do to correct any bacterial issues?

For the Beta Test, yes - I want to test both the fish and the water. It is my hope that for the real thing we can get away with testing just the water. Catching fish in a reef tank is so friggin hard.

What to do to correct bacterial issues... the amount of advice I can give depends on the issue.

If it is a question of diversity or nitrifying microbes (two of the most common goals reef keepers cite for adding bacterial supplements) there is good evidence that these can be increased by adding live sand, mud, or rock.

If a particular family of microbes if present at abnormally high or low levels, in some cases there is enough evidence in hand to recommend a solution. e.g. the family Pelagibacteraceae (the most abundant kind of bacteria found in the open ocean) appear to be depleted by use of a UV sterilizer. So if these levels are high or low, one could adjust their use of UV to adjust the levels of these bacteria. (I use this example only because there is a pretty clear relationship between this family and UV use)

In many other cases we are still learning how to adjust the levels. For these, I have to make the analogy to trace elements in an ICP report. If I were to find that Barium (for an arbitrary example) was extremely elevated in my tank, I dont know a specific treatment to reduce Barium levels. But I would still find it useful to know this, so that I could explore the reasons for this change and perhaps take broad general actions (like a large water change) to address it.

 

[Tony R.]

Hi everyone,

I've been testing the microbiomes of saltwater aquariums for about a year now, and one interesting thing I've noticed is that a reasonable fraction of reef tanks have one or more known fish pathogens. But they're not everywhere. I'm starting this thread to share these data with you, and discuss the possibility that undiagnosed bacterial infections may contribute to fish diseases and mortality in our aquariums.


The bacterial pathogens I have seen so far:

Pathogen	Prevalence (% of tanks)	Abundance, % of community median (range)	Disease (reference)	Known Susceptible Fish
Photobacterium damselae	14%	0.19% (0 - 1.3%)	Photobacteriosis and similar infections (Rivas et al. 2013, Andreoni & Magnani 2014)	Damsel family, others?
Piscirickettsia salmonis	1%	0% (0 - 0.13%)	Piscirickettsiosis (Rozas & Enrique 2014)	Salmonids, others?
Vibrio fortis	57%	0.16% (0 - 19%)	Enteritis (Wang et al 2016)	Seahorses, others?

A few important caveats about these findings:

• Genetic Variation - there is a lot of variation within each bacterial species in terms of virulence. For example, in P. damselae there are different sub-species and types with known differences in virulence and host ranges. However, the marker used here can't resolve these beyond the species level. Still, since so many of the sub species and types in this group are pathogens for fish or humans, I feel comfortable listing it as a pathogen.
• Unknown Susceptibilities - these pathogens are typically discovered in aquaculture settings, where a single species is grown. As a result, the researchers don't immediately document the range of susceptible fish in the aquarium trade, so we lack this information for most of these pathogens.

In other words, based on what we do not know for sure -- its possible that the specific bacteria detected here are non-pathogenic, close relatives of the known pathogens. Or its possible that even if they are pathogens, the kinds of fish kept in that tank may not be susceptible. With that said, I think we all agree that unless we manage diseases, fish deaths are pretty common in the hobby. So it seems prudent to look into these pathogens as possible contributing factor.

One finding I'd like to highlight is the wide range of abundance we see for some of these. For example, consider Vibrio fortis. This bacterium is present in over half the tanks I've tested, but typically at very low levels (median = 0.16% of the community). However, in one tank it made up 19% of the community, more than 100-fold higher in relative abundance than the median level. It seems plausible that this extreme variation could play a role in the extent of disease caused by these bacteria.

Another important factor to consider is resistance. Taking P. damselae as an example, research has shown that fish can become more resistant to this pathogen with age, and some fish show genetic advantages in resistance. So it is possible that fish in the tank are not affected, even if their species generally is susceptible.

My questions for the community:
1. Have you experienced fish diseases or deaths that you believe were primarily caused by bacterial infections?
2. What are your practices for managing bacterial pathogens in your tanks?

Thanks for reading, I'll be curious to hear your thoughts.

Fascinated by this line of thinking and the service you provide. I'm a molecular biologist working (by chance) in a marine invertebrate biology lab, one of the active areas of research we pursue is the commensal relationship between Vibrio spp. and shellfish (eastern oysters particularly). I'd love to know the set up you are running on your end, are you streaking and isolating colonies for target PCR validation or doing something more broad spectrum like environmental shotgun sequencing? Additionally do you do this in house or outsource your NGS, if in house that's hardcore! I'd love to geek out over the logistics sometime haha!

 

[AquaBiomics]

Fascinated by this line of thinking and the service you provide. I'm a molecular biologist working (by chance) in a marine invertebrate biology lab, one of the active areas of research we pursue is the commensal relationship between Vibrio spp. and shellfish (eastern oysters particularly). I'd love to know the set up you are running on your end, are you streaking and isolating colonies for target PCR validation or doing something more broad spectrum like environmental shotgun sequencing? Additionally do you do this in house or outsource your NGS, if in house that's hardcore! I'd love to geek out over the logistics sometime haha!

Hi Tony,
Sounds like we have a lot in common, I worked on Pacific oysters early in my career.

I don't do any "wet lab" microbiology at AquaBiomics, my service is based on DNA sequencing. I prepare amplicon sequencing libraries in house, and outsource only the sequencing itself. (Although my next step in my business growth will be to buy a new instrument that's just come out, that will allow me to do the whole thing in house. This will cut the turnaround time in half and in principle reduce cost per sample. Only need the money!)

Currently for the microbiome preps I'm targeting the V4 region (515-806) of the 16S rDNA. But this approach is easily expandable and multiplexable, so I can also at the same time target other markers, like an 18S marker for eukaryotic sequencing (fish parasites) and a plastid target for algal identification. The major bottleneck for all of this is only the time to test sensitivity of sampling.

Basically, I need more sick fish, parasite samples (e.g. AEFW) and nuisance algae!

 

[Jessican]

Any thoughts on bacteria and anemones? I have one variety of aquacultured BTA that is a prolific splitter (3 original BTAs have turned into 75+ in 1.5 years) and super healthy, but I can’t for the life of me keep any other variety of BTA. Doesn’t matter if they’re aquacultured or wild caught, large or small, they just wither away and die. I’m sure I’m grasping at straws, but could there be something about the bacterial makeup of my tanks that my original BTAs are immune to, that kills any new ones?

 

[trailermann]

It warms my heart to see you participating is this wonderful forum. Would it help to receive ANY fish that has died in my care, even if there are no signs of infections? I have had plenty the past few years.

 

[Montagne]

Unfortunately, today I inexplicably lost an apparently healthy fish I've had for 3 months after a week of lethargy and am wondering if I can send it to you as part of your BETA testing. Also unfortunately, its the second mature fish in 10 days and has stumped my LFS and reef2reef, so hoping someone can learn from this experience. Please reach out with details if you are interested, thank you

 

[Humblefish]

Unfortunately, today I inexplicably lost an apparently healthy fish I've had for 3 months after a week of lethargy and am wondering if I can send it to you as part of your BETA testing. Also unfortunately, its the second mature fish in 10 days and has stumped my LFS and reef2reef, so hoping someone can learn from this experience. Please reach out with details if you are interested, thank you

Did you freeze the body? You'd probably have to use ice and ship it overnight to prevent significant decay.

 

[Montagne]

Did you freeze the body? You'd probably have to use ice and ship it overnight to prevent significant decay.

I have it between wet paper towel in the fridge but can move it to the freezer.

p.s. I wrote out the full details of the progression over in the disease thread at https://humble.fish/community/index.php?threads/detectives-needed-what-is-killing-my-fish.2616/

 

[gunit]

I just received back a test result for a tank I am upgrading from that showed it had Photobacterium damselae. So that brings me to my questions:

1) The fish from that tank were already going to go through quarantine as an extra precaution. None are exibiting any symptoms but should I treat them prophylacticly before putting them into my new DT?

2) For the live rock from that tank or the tank itself, is there anything that can be done to it to make it "safe" again? Right now the old tank is fallow with just snails so I'm curious what, if anything, can/should be done.

 

[Humblefish]

1) The fish from that tank were already going to go through quarantine as an extra precaution. None are exibiting any symptoms but should I treat them prophylacticly before putting them into my new DT?

This study suggests you would need to use ciprofloxacin: First time isolation of Photobacterium damselae subsp. damselae from Caranx sexfasciatus in Persian Gulf, Iran

So, a bath treatment before the fish enter the new DT would be wise:

Ciprofloxacin (Best administered via 1-2 hour bath treatment. Dosage is high: 250mg per gal. Repeat every 24 hours for 7 days. Methylene Blue can be added to increase efficacy.)

2) For the live rock from that tank or the tank itself, is there anything that can be done to it to make it "safe" again? Right now the old tank is fallow with just snails so I'm curious what, if anything, can/should be done.

A UV does a pretty good job of eliminating bacteria in the water, but if the bacteria are inside the rocks you'd need to bleach them.

 

[AquaBiomics]

I just received back a test result for a tank I am upgrading from that showed it had Photobacterium damselae. So that brings me to my questions:

1) The fish from that tank were already going to go through quarantine as an extra precaution. None are exibiting any symptoms but should I treat them prophylacticly before putting them into my new DT?

2) For the live rock from that tank or the tank itself, is there anything that can be done to it to make it "safe" again? Right now the old tank is fallow with just snails so I'm curious what, if anything, can/should be done.

It may be useful to know what kind of fish we're talking about. Some groups are known to be susceptible, Id be more inclined to take action with those groups. Sadly we don't have any good list of groups that are known to *not* be susceptible.

P. damselae is free-living and associated with animals. I suspect very little of it is hanging out inside the rock but can't be sure. Washing the crap out of the rock seems like it couldnt hurt, and for a free living group like this it would offer a reasonable chance of getting rid of most of it.

 

[Badilac]

How long does it typically take to get a report back?

 

[Lexinverts]

How long does it typically take to get a report back?

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:

Sample Testing Queue

Products & Services | How it works | Order | Register Sample | Products & Services | How it works | Order | Reports | Register Sample | Account | Sample Testing Schedule Our testing operate…

aquabiomics.com

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.