New article on the microbial communities in saltwater aquariums

[AquaBiomics]

Hi everyone,

Most of us in the hobby are aware of the roles microbes play in our tanks, but very little information about these microbes has been available.

I wanted to bring to your attention a recent survey of microbial communities in home aquariums that we've recently completed. This analysis is based on DNA sequencing of water samples from hobbyist tanks. A few of the key findings:

• The water of established reef tanks contains several hundred different kinds of microbes (400, on average).
• These include microbes with known roles in maintaining water quality, and also known pathogens.
• The microbiome of a typical aquarium is dominated by a few families that are also among the most abundant in the ocean.
• The aquarium microbiome is mostly composed of Bacteria, but some of the few Archaea present have important roles in maintaining water quality.

There are endless questions left to answer in this field... this survey provides a baseline for understanding the typical aquarium microbiome. In future experiments and articles, I'll explore how we can best establish and adjust the microbiome in our aquariums.

You can read more here. I'll be curious to hear what you think!

-Eli

The relative abundance of each family in the core microbiome of a typical saltwater aquarium.

 

[Oldreeferman]

Thank you for presenting this for everyone in the reefing community,
I really enjoyed the presentation & layout of the experiments & samplings, especially with respect to the fact that i actually understood it, without having to first have a masters in marine biology, DNA sequencing, and microbiology study to comprehend what was being explained. That component of research is extremely heady & could have gotten really complex & hard to understand fast had it been interjected into the bulk of the presentation. ( I really app that you did not do that, tho could have as many do & wrote it in understandable language instead.... that i could absorb, thank you).
Instead of falling asleep over complex explanations of the machinery of the science involved you explained mainly the results and kept me on the edge of my chair wanting more to read.
Im really looking forward to the next experiments & articles in the future, especially in relation to possibly modifying the microbiome, maybe even effecting and/or modifying micro algae and possibly cyanobacteria growths etc...and the pathogens have my attention also.

My only question is, do you have any sort of timeline when you think the next presentation might possibly be ready, as i realize this type of study/work takes lots of effort & time to do, then place into a presentation article format.

Thanks again for sharing your results,


Dave

 

[AquaBiomics]

Hi Dave,

Glad you enjoyed it! It can be challenging translating science into English so I am happy to hear it succeeded for someone.

I have two more articles available now.
Different reef tanks have different microbes
How to establish the microbiome using live rock

Hope these are interesting and useful for the community,

-Eli

 

[five.five-six]

Awesome!

My son is struggling with 10th grade biology which means that I am taking 10th grade biology again so I really appreciate the abstract presented in the first post because after my 60hr weeks and 10th grade biology class, the last thing I want to do is read and digest a captive marine biology study.


So, let me say thank you for your work, it appears fairly comprehensive. I have a hypothesis that pests like Cyanobacteria and dinoflagellates overpopulate either wholly or in part due to a retarded population either competing and or predatory microbes. Did you or could you identify microbiome irregularities in tanks suffering from dinoflagellate infestations? If you do find a causational correlation with a few key species of dinoflagellates I'm sure you could make some real money with a remedy. Dinoflagellates can be a tank killer.

 

[HumbleFish]

Is there any way to DNA test for various parasites and worms sometimes found in a SW aquarium?

 

[AquaBiomics]

Is there any way to DNA test for various parasites and worms sometimes found in a SW aquarium?

The answer has two parts:
1. The easy part - if we can get DNA from a known eukaryotic parasite into the sample, we can detect and identify it with a simple modification to this test. This could mean living cells or just free DNA ("environmental DNA"), both of which are captured on the filters.

There are well established PCR primers (pieces of synthetic DNA used during sample preparation) that amplify a similar genetic marker more or less universally in eukaryotes, and the sequences of the known parasites are in the databases. So the lab part is fairly straightforward.

2. The harder parts - we still need to establish the sensitivity required (i.e. how much tank water do we need to sample to detect that Cryptocaryon is present in the tank?) The main challenge here is access to diagnosed, sick, but still living fish, and water samples from their tanks.

 

[HumbleFish]

The answer has two parts:
2. The harder parts - we still need to establish the sensitivity required (i.e. how much tank water do we need to sample to detect that Cryptocaryon is present in the tank?) The main challenge here is access to diagnosed, sick, but still living fish, and water samples from their tanks.

I've got the same problem. Some new treatments I'd like to test out, but finding sick (yet still viable) specimens to experiment on can be hard to find. Or it's hard to swallow paying full retail price for a fish that might die in the bag on the way home.

 

[AquaBiomics]

I have a hypothesis that pests like Cyanobacteria and dinoflagellates overpopulate either wholly or in part due to a retarded population either competing and or predatory microbes. Did you or could you identify microbiome irregularities in tanks suffering from dinoflagellate infestations? If you do find a causational correlation with a few key species of dinoflagellates I'm sure you could make some real money with a remedy. Dinoflagellates can be a tank killer.

Absolutely, I think the idea of competition or even more direct interactions between bacteria & dinoflagellates makes sense, and I know theres been quite a bit of experimental work in the hobbyist community in an effort to get rid of dinos by manipulating microbial populations.

Every client is asked to complete a short web survey when they send in their sample, and the questions include tank problems like dinoflagellates. So as the size of the database grows, it will become possible to ask questions like "Are there any groups of microbes that are always rare or absent when dinoflagellates are present?"

The DB is just getting to the size where I'll start to believe conclusions that emerge from these tests, so I am working on this and related questions in the near future.

 

[AquaBiomics]

I've got the same problem. Some new treatments I'd like to test out, but finding sick (yet still viable) specimens to experiment on can be hard to find. Or it's hard to swallow paying full retail price for a fish that might die in the bag on the way home.

Yeah, its funny how working on aquarium microbes has changed my perspective. A couple times I've ordered a batch of fish from a wholesaler or importer hoping to find some diseased ones, and ended up oddly disappointed when they were all healthy.

On the other hand, I recently discovered that one of my experimental tanks caught Aquarickettsia rohweri, a fairly newly discovered coral pathogen, and I was thrilled. "Finally, I can do some experiments with this bug!"

Still do everything I can to keep my pets healthy but now when I find something diseased in an order, the first thing I usually say without thinking is "oh cool, I need to take a sample of this"

 

[HumbleFish]

Yeah, its funny how working on aquarium microbes has changed my perspective. A couple times I've ordered a batch of fish from a wholesaler or importer hoping to find some diseased ones, and ended up oddly disappointed when they were all healthy.

Most wholesalers run therapeutic copper (or utilize some other management tool) to keep parasites at bay. They're still on some of the fish, but you'd have to do random skin & gill scrapes to find them. It usually takes 2-4 weeks in non-medicated water for a full outbreak to occur.

I would checkout your local Petco to find diseased fish. Some of the more sensitive species will die soon after hitting their tanks. However, they often have cardinals, chromis, clownfish, grammas, tangs and other hardy fish that are showing full blown symptoms but their immune system is managing it. These are the perfect fish to experiment on.

 

[AquaBiomics]

Most wholesalers run therapeutic copper (or utilize some other management tool) to keep parasites at bay. They're still on some of the fish, but you'd have to do random skin & gill scrapes to find them. It usually takes 2-4 weeks in non-medicated water for a full outbreak to occur.

I would checkout your local Petco to find diseased fish. Some of the more sensitive species will die soon after hitting their tanks. However, they often have cardinals, chromis, clownfish, grammas, tangs and other hardy fish that are showing full blown symptoms but their immune system is managing it. These are the perfect fish to experiment on.

Good idea. I knew there was a place for Petco in our hobby!

You're right, a fish with visible symptoms is what I need for some of my tests, so its probably worth paying retail for a few of the cheaper fish.

 

[Oldreeferman]

I agree as every Petco ive visited were all holding some sick fish & they share a main water source i was told by an employee, so its in all the marine tanks, most all tanks had red cyano and cases of ick. Couldn't pay me to put anything from there in my tanks without a serious QT. Great place to get your patients tho for sure.