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

[AquaBiomics]

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

 

[vetteguy53081]

 

[twentyleagues]

Welcome!

 

[Stephen8169301]

 

[JC1977]

 

[beesnreefs]

Glad to have you back on the forums, Eli! Big fan of the important work @AquaBiomics is doing

 

[BrotatoSalad]

Welcome back! Excited to see your posts and contributions.

 

[jsker]

Welcome back and nice meeting you

 

[dstockwell]

Welcome back

 

[shakacuz]

welcome back aboard the r2r board!

 

[SPR1968]

Welcome back!

 

[cpschult]

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

How are you quantifying the bacteria without enumeration?

 

[danenelsen]

 

[biophilia]

Welcome back Dr. Meyer!

The work you're doing is really fascinating. Years back, I read "Coral Reefs in the Microbial Seas" by Rohwer and Youle and it really shaped how I think about reef aquariums, and corals in general. You're offering a new lens, and sense of scale, to hobbyists that I think is super fascinating and important. So much life that goes unseen and under-appreciated in reef tanks.

One thing I've wondered: do you have any insight regarding changes in bacterial communities (especially pathogenic) in systems that are employing heavy organic carbon dosing?

For example: I run some NPS tanks at a public aquarium and have considered ramping up carbon dosing as a bacteria food source for corals and sponges and also to control nutrient levels, but have concerns about fueling pathogenic bacterial growth in a system with such high nutrient inputs.

 

[marcinpolak]

 

[Nano_Man]

 

[JZ199]

Welcome back!!

 

[AquaBiomics]

How are you quantifying the bacteria without enumeration?

Sequencing provides information on the relative abundance. The fraction of the community that each type contributes to the total.

Every method has pros and cons; it is true that sequencing does not provide direct measurements of absolute abundance (cells per ml). Microbiologists still find these methods very useful, and the kind of sequencing we're doing here is widely used throughout environmental and biomedical research. But the limitation you bring up is an important one to keep in mind when interpreting the results.

 

[AquaBiomics]

Welcome back Dr. Meyer!

The work you're doing is really fascinating. Years back, I read "Coral Reefs in the Microbial Seas" by Rohwer and Youle and it really shaped how I think about reef aquariums, and corals in general. You're offering a new lens, and sense of scale, to hobbyists that I think is super fascinating and important. So much life that goes unseen and under-appreciated in reef tanks.

One thing I've wondered: do you have any insight regarding changes in bacterial communities (especially pathogenic) in systems that are employing heavy organic carbon dosing?

For example: I run some NPS tanks at a public aquarium and have considered ramping up carbon dosing as a bacteria food source for corals and sponges and also to control nutrient levels, but have concerns about fueling pathogenic bacterial growth in a system with such high nutrient inputs.

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.

 

[c_healy]

Welcome back. I recall reading some of your posts back in the day. I look forward to reading your future posts.