(Back To The Forum) I run an Aquarium DNA testing company, AMA

[kevgib67]

Welcome back Eli, glad you are here!

 

[biophilia]

We do see signatures of carbon dosing in hobbyist aquariums. A few families that we well known to respond to nutrient dosing from the literature, also are present at high levels in many tanks that carbon dose.

When we look at these tanks at the species level we often find that carbon dosing promotes the growth of specific bacteria associated with the fish gut microbiome. In other words, in a heavily carbon dosed tank the dominant bacteria are often fish poop bacteria. But those are not pathogens, they're normal members of the fish gut community even if they're not normally present at high levels in the water.

We don't generally see increased Vibrionaceae or Rhodobacteraceae in carbon dosed tanks. This may suggest we shouldnt worry too much about carbon dosing in terms of pathogens. On the other hand, we do sometimes see elevated Alteromonadaceae which is a group that includes some pathogens, and a group where standard genetic markers have limited resolution. So I can't rule it out, only say that its not the major effect we find.

In general, carbon dosing appears to heavily alter the community and for that reason I think it should probably be used more cautiously in the hobby than it currently is. It sounds like you're approaching this with the appropriate level of caution.

I especially am not a fan of hidden carbon in many aquarium products that don't list their full ingredients. Its not that I'm saying noone should add any carbon - just that the type and amounts have a very large impact on the bacterial community so my gut feeling is we should probably be as cautious about adding carbon to our tanks as we are when adding any other nutrient.

None of this is intended to say "don't carbon dose the system you mentioned" -- just my thoughts on carbon dosing in general based on what we've seen in these data.

Thank you! This is really great insight.

 

[Jimbhoy13]

Welcome back to R2R Eli. Your knowledge will be very useful here.

 

[Just John]

Welcome back!

That's COOL STUFF you're doing!

 

[Gumbies R Us]

Welcome to Reef2Reef!!!

 

[G Santana]

Welcome back to the Reef

 

[907_Reefer]

Welcome!

 

[CoralB]

Welcome !!!

 

[Keko21]

 

[Buckster]

Hello and Welcome back to posting!

 

[Wolf8895]

Welcome back! Look forward to reading more.

 

[StubbyAcro]

We do see signatures of carbon dosing in hobbyist aquariums. A few families that we well known to respond to nutrient dosing from the literature, also are present at high levels in many tanks that carbon dose.

When we look at these tanks at the species level we often find that carbon dosing promotes the growth of specific bacteria associated with the fish gut microbiome. In other words, in a heavily carbon dosed tank the dominant bacteria are often fish poop bacteria. But those are not pathogens, they're normal members of the fish gut community even if they're not normally present at high levels in the water.

We don't generally see increased Vibrionaceae or Rhodobacteraceae in carbon dosed tanks. This may suggest we shouldnt worry too much about carbon dosing in terms of pathogens. On the other hand, we do sometimes see elevated Alteromonadaceae which is a group that includes some pathogens, and a group where standard genetic markers have limited resolution. So I can't rule it out, only say that its not the major effect we find.

In general, carbon dosing appears to heavily alter the community and for that reason I think it should probably be used more cautiously in the hobby than it currently is. It sounds like you're approaching this with the appropriate level of caution.

I especially am not a fan of hidden carbon in many aquarium products that don't list their full ingredients. Its not that I'm saying noone should add any carbon - just that the type and amounts have a very large impact on the bacterial community so my gut feeling is we should probably be as cautious about adding carbon to our tanks as we are when adding any other nutrient.

None of this is intended to say "don't carbon dose the system you mentioned" -- just my thoughts on carbon dosing in general based on what we've seen in these data.

Thank you Dr Eli. I've been wondering and searching for answer about this for a very long time. Even after reading dozens of good stories of vinegar dosing, I still can't help but worried that it might fuel some pathogenic bacteria. Although my vinegar dosing routine won't change, this post really put my mind at ease.

 

[paragrouper]

Hi Eli and welcome back

 

[JamesTh]

Welcome back @AquaBiomics

I’m certainly not an expert on this, but I think so little is really known by the average person that has their own reef tank about the types and role of bacteria within their reef tank, obviously myself included.

so, I have some questions for you, please:

1) what are your general thoughts of the general bacterial additives that are available to add to our tanks, please? I’m thinking of products such as fauna Marin bacto-blend, bacto-balance, TNS pro-bio, along with all the other bacterial products available from other suppliers too really.

2) would you say that they’re generally beneficial to dose, or do you think that a tank should just be allowed to sort itself out, bacterially speaking?

3) if I go ahead and buy a bacterial test from you guys, then what useful information can I expect to get from it, please? I can well imagine that I find out a certain percentage of my water contains bacteria a, b, and c. But what can I do with that information, on a practical level? Do I actually need to care what the results are?

Thank you!

 

[Dburr1014]

We do see signatures of carbon dosing in hobbyist aquariums. A few families that we well known to respond to nutrient dosing from the literature, also are present at high levels in many tanks that carbon dose.

When we look at these tanks at the species level we often find that carbon dosing promotes the growth of specific bacteria associated with the fish gut microbiome. In other words, in a heavily carbon dosed tank the dominant bacteria are often fish poop bacteria. But those are not pathogens, they're normal members of the fish gut community even if they're not normally present at high levels in the water.

We don't generally see increased Vibrionaceae or Rhodobacteraceae in carbon dosed tanks. This may suggest we shouldnt worry too much about carbon dosing in terms of pathogens. On the other hand, we do sometimes see elevated Alteromonadaceae which is a group that includes some pathogens, and a group where standard genetic markers have limited resolution. So I can't rule it out, only say that its not the major effect we find.

In general, carbon dosing appears to heavily alter the community and for that reason I think it should probably be used more cautiously in the hobby than it currently is. It sounds like you're approaching this with the appropriate level of caution.

I especially am not a fan of hidden carbon in many aquarium products that don't list their full ingredients. Its not that I'm saying noone should add any carbon - just that the type and amounts have a very large impact on the bacterial community so my gut feeling is we should probably be as cautious about adding carbon to our tanks as we are when adding any other nutrient.

None of this is intended to say "don't carbon dose the system you mentioned" -- just my thoughts on carbon dosing in general based on what we've seen in these data.

Welcome back Dr.
I have read some pros and cons to the work you are doing. But that is how a lot of changes in the reef hobby get going. Thank you for your contributions!

I'm this response you noted fish gut bac was high in carbon dosed tanks and members of Vibrionaceae and Rhodobacteraceae were low.
Are you saying some bacteria are out competing others altering the numbers? Or you can't do a count, your just not seeing much in the samples.

 

[1112-425XL]

Welcome Back, keep the questions coming... Good Stuff!

 

[RedReefer]

Welcome back to R2R!!!

 

[LRT]

Hi again Reef2Reef,

I used to post here a lot but have been away from forums for a couple years. I thought I'd re-introduce myself here since the community has probably grown a lot since I was here last.

I'm a professional biologist and recovering academic. I live in Oregon's beautiful Willamette Valley with my wife, 3 kids, a bunch of farm animals, and more reef tanks than I'd care to admit in polite company. (only one display tank in the house, but theres that whole greenhouse I built to house coral tanks too...)

After a couple decades in the research world using DNA sequencing to study corals and a variety of other odd creatures, I started a DNA testing company a few years aiming to bring these same methods to the aquarium hobby. We've been running samples for the reefkeeping community ever since, and this has grown into my full time job and primary source of support.

Over the past 4 years we've gathered lots of data on the microbial community in reef tanks. We've also built a database of eukaryotic parasites including those that cause some of the most common fish diseases. Some of our earliest findings I wrote up on these forums, but as we grew I ran out of time for these writeups. I hope to change that in the near future. A few teasers to share:

• The bacteria associated with the coral disease SCTLD appear to be causing disease in Acropora and other SPS in the hobby, but some of our clients have promising data on a possible treatment
• We're finding Myxozoans, an unexpected group of fish parasites that hadnt previously been discussed much in the hobby - the jury's still out on whether they're causing fish mortality in the hobby, but they're a nasty parasite in fish aquaculture...
• We've come across a variety of other interesting parasites like the Amoeba that cause Amoebic Gill Disease, or the toxic dinoflagellates Pfiesteria

In some ways our findings contradict a theory many had suggested before DNA sequencing was available, that all tanks probably contain parasites like Cryptocaryon (Ich). On the other hand, we find a variety of other, sometimes unexpected parasites. There's a lot more than just Ich out there! (of course, we do find plenty of Cryptocaryon too. Especially since over the past few months we've improved the sensitivity of our tankDNA test; I suspect our estimate of ~10% prevalence will continue to climb).

When I came back to the forums I came across a few pretty negative comments about various aspects of this technology or our service. Its a new technology for reef keeping, and skepticism can be natural and appropriate when something new comes up. I would be happy to answer any questions and attempt to relieve any concerns.

We test reef tank DNA for a living. Ask me anything!

-Eli

This is awesome glad to see you back!
Have you done a thread or compiled data on the most common bacteria your seeing in thriving healthy tanks? Can you stear me in the right direction or share your observations on what you have found?
Same as far as infected corals and/or unhealthy systems?
Lastly, have you done any more testing with antibiotics or medicines on bacteria found in unhealthy systems and found medicines that treat specific bacterias found in infected corals or systems?
I'm very intrigued and there has been a ton of discussion on this topic lately and would love to hear where all this sits at this point.

 

[Hats_]

My university does research on the urchin problem in caribbean, seems to be a certain type of ciliate that causes the urchins to die off, have you ever encountered something similar in your research?

 

[AquaBiomics]

Have you done a thread or compiled data on the most common bacteria your seeing in thriving healthy tanks? Can you stear me in the right direction or share your observations on what you have found?

After looking at aquarium microbiomes for almost 5 years now, a few themes have become crystal clear.

• Theres definitely a typical microbiome that emerges over time in healthy mature tanks.
• Its generally dominated by planktonic, open-ocean bacteria from the family Pelagibacteraceae.
• A few pathogens detectable in the water sample are clearly associated with coral disease (e.g. Arcobacter sp. with BJD).

I'm way behind on writing this up. There are some early threads linked here
https://aquabiomics.com/articles

More recently I've starting a database of things we find in aquarium DNA samples.

Info – AquaBiomics

Information about the microbes found in aquarium DNA samples

aquabiomics.com

Its still a work in progress, there are always more families to add. Its intended for clients interpreting their results, or anyone interested in reef tank microbes and parasites.

Hope this is useful!