This is what I've dreamed of for so long! Testing for microbes in our tanks!

[sixty_reefer]

This is the #1 question that experienced reefers ask me. "What can I do about it?"

To specifically answer your question about Vibrio, I am not currently testing chloramphenicol because my reading suggests it is not specific enough. I am testing another more specific medication for Vibrio, but it is early in R&D. I can make no promises until I have data to support them.

My vision is not to repackage and sell chloramphenicol, or other simple treatments or additives like this. If that turned out to be the key medication, it could be readily bought in the internet age. After recently setting up a molecular biology lab independently, I will say Its amazing what you can buy on amazon these days

My vision is instead to enable the experiments that will teach us which additives or practices establish a beneficial community, or correct problems in an unhealthy community. I'm running some of these experiments, but I also know that there are experiments underway across the community. Now that the measurements are available, I don't think it'll be long before we all learn collectively what makes a healthy microbiome, and how to establish one.

Has a connection been made so far on tanks with dinoflagellates or Cyanobacteria outbreaks having less microbe diversity?

 

[AquaBiomics]

Has a connection been made so far on tanks with dinoflagellates or Cyanobacteria outbreaks having less microbe diversity?

There is a trend in my first survey of established reef tanks, but its not statistically significant. Tanks with Cyano problems had 25% lower diversity on average than tanks without Cyano problems. But again, not statistically significant, so we can only say this suggests an association. If its a real difference, it should become significant as we add more samples to the database.

In my replicated tank cycling experiments (I am really almost done with this article now) I found a striking effect. Night and day. The live rock treatment that produced high diversity also avoided ugly algae blooms, and the sand has remained white for the entire 6 months theyve been established. The dry rock tanks went through all the ugly stages you'd expect and remain ugly today (I have not analyzed these algal communities).

More data are needed (and I need to finally finish writing this thing up) but I see these tanks every day in my lab. I can't escape the conclusion that the different bacterial communities in these tanks are the cause of the visible differences in these tanks...

 

[sixty_reefer]

There is a trend in my first survey of established reef tanks, but its not statistically significant. Tanks with Cyano problems had 25% lower diversity on average than tanks without Cyano problems. But again, not statistically significant, so we can only say this suggests an association. If its a real difference, it should become significant as we add more samples to the database.

In my replicated tank cycling experiments (I am really almost done with this article now) I found a striking effect. Night and day. The live rock treatment that produced high diversity also avoided ugly algae blooms, and the sand has remained white for the entire 6 months theyve been established. The dry rock tanks went through all the ugly stages you'd expect and remain ugly today (I have not analyzed these algal communities).

More data are needed (and I need to finally finish writing this thing up) but I see these tanks every day in my lab. I can't escape the conclusion that the different bacterial communities in these tanks are the cause of the visible differences in these tanks...

Thank you for taking the time I find that your work will definitely help us to understand the hobby better. I’ve only asked the question as it is a suspension I have but never before was able to connect it, hopefully soon you could do some work on it as it would benefit the hobby we all adore.

 

[Randy Holmes-Farley]

Randy the main two reasons I dose bacteria are because my heavy skimming and possible predation. I feel like my skimmer is pulling out some of my bacteria population. I also think some of our bacteria are being consumed by other organisms. My tank seems off sometimes and when I dose bacteria it improves. This could be because the bacteria population was low and has now been replenished again. Or... the bacteria removed some of the organic matter and N&P. Either way, you should pick up a bottle of Waste Away or Eco Balance Wink Wink Refresh is good too. Dr. Tim’s products work!

I boosted bacteria by dosing vinegar.Bacteria are a good food for filter feeders such as sponges. That’s part of the reason I used vinegar. I just don’t see a reason to add bacterial products except in special circumstances.

 

[Reefahholic]

I boosted bacteria by dosing vinegar.Bacteria are a good food for filter feeders such as sponges. That’s part of the reason I used vinegar. I just don’t see a reason to add bacterial products except in special circumstances.

That’s good man, Lou from Tropic Marin said that he’s a fan of carbon dosing. He said that the bacteria consume the phosphates and the coral consume the bacteria which gets the phosphate into the coral easily since they have a harder time consuming phosphate rather than nitrates. Since he talked about this...I started using Reef Actif from time to time and so far so good. Probably should use it 24/7, but trying to balance nutrients can be quite challenging.

 

[Dr. Bull]

There is some real scientific research being done in this area right at the Shedd Aquarium in Chicago. I highly suggest if your in the Chicago area to drop by and take the "Behind the Scenes" tour for an extra 20 bucks. I did this about a month ago and got lucky enough to be the only one on the tour. Currently they claim to be the only public aquarium with a microbiology lab on site, and will take you by it during the tour. One of the biologists was kind enough to drop what he was doing and come out and chat with me for about 15 mins. He also printed me off copies of their two most recent publications on the subject for further reading. You can find the abstracts with unrestricted links to free copies of the actual publications here:

https://www.ncbi.nlm.nih.gov/pubmed/26031788

https://www.ncbi.nlm.nih.gov/pubmed/28713358

 

[Scubabum]

@Scubabum why you gotta confuse me refkpr! I tried to @ your name and it didn’t pop up. Lol.

So how did the results turn out with running the maintenance dose of Waste Away? Interested to see the results. I started using Eco Balance as well. Not scheduled, but just when I feel the tank could benefit.

I wonder how Prodibio would test? Will it beat Dr. Tim’s or Not? Hmm....

Sorry to confuse you. I had an account under Reefkpr but lost access. Anyway I haven't received any results back. I'll be sure and post when they arrive.

 

[Reefahholic]

Sorry to confuse you. I had an account under Reefkpr but lost access. Anyway I haven't received any results back. I'll be sure and post when they arrive.

Sounds good brotha'...standing by. Interested to see how this unfolds with data across the board with both new and older established systems. My guess is that skimmers and filter socks likely pull out more than we think. Even if you're only running 200 micron....give it a week...you now have a 10 micron. Lets not forget about predation. Other microorganisms can eat our beneficial bacteria as well.

 

[brandon429]

Dr. Bull I thought those were great reads. Anytime I see an article describing effects from complete / 90% water changes, I’m secretly wondering how their data is going to align with twenty years of pico and nano reef systems with sps / lps fish etc who’ve been doing them the whole time. We can see the effects, they’re great effects.
its why people keep using the option. Each time I open a link I’m getting ready for some description of imbalance, problem etc

none of the articles I’ve read about biome impact describe long terms detriment. Neat

systems self regulate given basic exchange, and tend to imbalance and need dosers both chem and bio when exchange slows or stops


this aligns with twenty years of data, if it didn’t we would need to chat with the article writers to see how those effects documented online relate to the findings. It’s nice to see the mechanisms described in those articles explaining why full water change has worked so well.

when we keep reefs free of or at least low/managed detritus loading, and decent turnover or exchange in some manner, they self regulate. two hundred thousand no problem no invasion nano reefs can attest.
Bio imbalance and buying target pro biotics is for large tankers or tinkerers, inaccessible large water columns
Studying and manipulating bacteria is the way of the future it’s all amazing and large tanks needs help as they can’t easily replace everything

I still like how the old cheap free method remains a contender though, among choices at least when dealing with smaller tanks that can run a full change. Systems started with real live rock have a lucky advantage in that they start with an incredibly diverse microbiome vs having to dose and measure up to one

its pretty amazing to consider the number of reefs truly in misalignment from using dry rock starts. There is a need for this science and that big picture makes live rock stand out as gold

 

[reefwiser]

 

[lexinverts]

Great interview! I think you found a good MACNA speaker @reefwiser

 

[AquaBiomics]

Thanks again, Ed, it was fun talking with you and I appreciate the chance to share some information about the service.

 

[AquaBiomics]

There is some real scientific research being done in this area right at the Shedd Aquarium in Chicago. I highly suggest if your in the Chicago area to drop by and take the "Behind the Scenes" tour for an extra 20 bucks. I did this about a month ago and got lucky enough to be the only one on the tour. Currently they claim to be the only public aquarium with a microbiology lab on site, and will take you by it during the tour. One of the biologists was kind enough to drop what he was doing and come out and chat with me for about 15 mins. He also printed me off copies of their two most recent publications on the subject for further reading. You can find the abstracts with unrestricted links to free copies of the actual publications here:

https://www.ncbi.nlm.nih.gov/pubmed/26031788

https://www.ncbi.nlm.nih.gov/pubmed/28713358

Thanks for bringing these up. These are some of the few real peer reviewed studies I'm aware of in the aquarium environment - most of this work gets done out in the big messy ocean.

The water change paper is pretty dramatic, and is the reason I advise clients to sample their aquarium before doing any major maintenance rather than after

Itd be fun to repeat those measurements at some point with smaller water changes. Something I wonder about is daily tiny changes (AWC) versus period larger changes. In principle both can achieve the same average chemistry, but it seems plausible that small daily AWC could promote a more stable microbiome.

 

[Mortie31]

I’d be interested to know how bacteria levels change over time in a stable aquarium. Maybe samples taken daily over a 3 month period, for me there is little point in a snapshot sample if it’s results are meaningless in a matter of days. If you have already done this could you share the results please.

 

[AquaBiomics]

I’d be interested to know how bacteria levels change over time in a stable aquarium. Maybe samples taken daily over a 3 month period, for me there is little point in a snapshot sample if it’s results are meaningless in a matter of days. If you have already done this could you share the results please.

Long term stability is an interesting question. Of course it takes a long time to gather long time series... so no, those data are not available yet.

I've just finished an article that I'll be posting shortly here on R2R that includes weekly samples during establishment of new aquariums. I think you'll find these data interesting and relevant for your question. Even during the dynamic stages of a new aquarium, the microbiome doesnt change on a day to day basis. The community in a tank stays pretty similar at least over the course of a few weeks.

And Im in the lab now finishing up the current batch of samples, which includes tanks I sampled ~6 months ago. So we'll get a first look at long term stability in established tanks soon.

An important caveat for those results, though, will be whether the owners left the tanks unchanged during the intervening time. How many of us can avoid tinkering with our tanks for a whole 6 months?

 

[Mortie31]

Long term stability is an interesting question. Of course it takes a long time to gather long time series... so no, those data are not available yet.

I've just finished an article that I'll be posting shortly here on R2R that includes weekly samples during establishment of new aquariums. I think you'll find these data interesting and relevant for your question. Even during the dynamic stages of a new aquarium, the microbiome doesnt change on a day to day basis. The community in a tank stays pretty similar at least over the course of a few weeks.

And Im in the lab now finishing up the current batch of samples, which includes tanks I sampled ~6 months ago. So we'll get a first look at long term stability in established tanks soon.

An important caveat for those results, though, will be whether the owners left the tanks unchanged during the intervening time. How many of us can avoid tinkering with our tanks for a whole 6 months?

Thanks for replying, I think your findings on this will be interesting, as to me it’s the long term stability that is crucial, and if/ by how much the bacterial levels change. I agree one problem we have to face is the constant fiddling and how doing this impacts either positively or negatively, or indeed does the balance change naturally without our intervention and if this occurs does it reduce as tank ages or is there a constant shifting of predominance, depending say on nutrient levels. Thanks for the good work I look forward to your discoveries, sadly I’m a little to far away to use your lab..

 

[taricha]

I've just finished an article that I'll be posting shortly here on R2R that includes weekly samples during establishment of new aquariums.

excited to read.

 

[taricha]

The dry rock tanks went through all the ugly stages you'd expect and remain ugly today (I have not analyzed these algal communities).

I seriously doubt it's needed, but if you wanted any help with microscope IDs of the algal communities, some of us would be very interested to help.

 

[AquaBiomics]

I seriously doubt it's needed, but if you wanted any help with microscope IDs of the algal communities, some of us would be very interested to help.

Thanks, I must say I have not invested in a microscope yet for this new lab (not really useful for the microbiome work)... but I agree when it comes time to ID those algae we should do both morphological and sequence based ID. (I always favor DNA data because its easier to make computers do the work for me!) I'll have to look into a low cost microscope...

Recently I have put R&D on the back burner while I processed client samples but the latest batch goes out for sequencing today, so now I get to work on experiments again. Algal ID is on the list along with carbon dosing and further work on coral antibiotics.

 

[Reesj]

Would love to see soem results from the people who were sent test samples btw. Been few weeks without any..