How stable is the aquarium microbiome? (A peer-reviewed, open-access study)

AquaBiomics

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Hi everyone,

I’m writing to bring to your attention a recent article entitled “Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria”. I don’t think we’ve discussed this study yet on R2R, but it’s directly relevant for many of the questions that are often brought up here. Fortunately this one is open-access, so you can read the whole thing here or download the PDF here.

This is the only peer-reviewed study of its kind that I know of, conducted by some of the leading experts in the use of these methods to study microbial communities. The first author, Holly Bik, has done a lot of really interesting work using DNA sequencing to study communities of various kinds. And the corresponding author, Jonathan Eisen, is a giant in this field who has played important roles in the Human Microbiome Project and other large microbiome projects.

The authors used DNA sequencing to study the microbial communities in aquarium water and surfaces (sound familiar?) They established and maintained a pair of large aquariums following what they deemed standard or best practices among aquarists. They sampled the microbial communities in these tanks repeatedly for about two months, to evaluate how the communities changed in response to actions by the aquarists.

Bik and coauthors found that
  • Aquarium microbiomes remain generally stable during regular aquarium maintenance
  • However, large disturbances can produce lasting changes in the community
  • The addition of live rock rapidly produced diverse communities that resemble established aquariums
  • This effect provided functional nitrifying communities at levels similar to established tanks
  • Later addition of different live rock led to substantial changes in the microbiome
In a lot of ways this study confirms what hobbyists have known for a long time, and what I reported in my live rock study. (Which is reassuring, since they method they used here is essentially the same as AquaBiomics testing of home aquariums). But what’s really cool here is that they followed these aquariums for two months, testing the microbiome every few days. This allowed the authors to monitor changes in these communities at a fine time-scale.

They found that the communities of microbes in saltwater aquariums remain relatively stable unless we do something specifically to alter them. This long stable period (from about Dec 15 to Jan 14) is readily visible in the following figure. And it shows that our actions, as aquarists, can have lasting effects on the microbiome of our tanks. See for example the dramatic changes in community composition after addition of live rock on Dec 12 and Jan 14 in this figure.


The most interesting part, for me, is the authors’ emphasis on “alternative stable states”. These communities generally remain stable, until disrupted by some action of the aquarist. Our actions can produce lasting changes in these communities, by shifting the community from one stable state to a different stable state. By repeatedly sampling a few tanks over the course of two months, the authors were able to observe the systems as they changed from one state to another.

This reminds me of the patterns I’ve described by surveying multiple hobbyist tanks. Aquarium microbiomes fell into a few clear clusters. These snapshots suggested that over time aquariums converged on one of a small number of patterns. Bik and her coauthors' study provides further support for this idea that there are alternative stable states in aquarium microbiomes.

One of these transitions (the first additional of live rock) clearly produced stable and beneficial changes in the microbial community. The second transition (additional live rock added at a later time) also affected the community, but the authors caution that (a) this transition was not accompanied by any measurable differences in function, and (b) further sampling would be needed to evaluate the stability of this second transition.

This later addition of live rock to an existing tank is something many people have asked me about. This study by Bik and coauthors shows evidence that this practice alters the microbial community. And I’ve recently described my own experience supplementing my home tanks with live sand and mud, showing that other (often much cheaper) materials can do similar things.

So the communities exist in a few different states, and we can shift the community between them depending on what we add, but the great question remains – what are the functional consequences of these different states? As the authors note at the end,
Bik et al. said:
Future studies of aquaria should also … quantify the effects of specific perturbations. Aquaria represent an ideal mesocosm system that can be easily leveraged to test diverse biological hypotheses. (emphasis mine)
I will note here that the hobbyist community is conducting many thousands of experiments on this subject right now, with all the different products people are dosing in their tanks. The authors emphasize that we need to quantify the effects of these treatments. They only had two aquariums for this study, but with your (collectively) thousands of successful reef tanks, I think we’re in a good position to do exactly this. So let’s get to measuring!
 

brandon429

why did you put a reef in that
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a recent large change to track for bad outcomes. Pls see if the article authors can see Jon’s work


when you say large changes above, what Jon did on file is the largest change one can do to a reef tank. Not anything they could do would be a larger systemic change than that action


will corals wither and starve, or prosper?

It’s nice to have extreme examples on hand. *bacterial changes would have to follow such a flushing event* and now we can see if those changes are good or bad for the system.

Jon’s example is testing how much bacteria one can scale back at once, and still maintain the same or better coral production rates.

all roads in reefing seem to be leading to probiotic supplementation $ we need to keep an eye out for that new sales angle


in my opinion Jon should be contacted and offered a free tank dna sampling, we want to see post rip clean data on a flourishing reef.
 
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reeferfoxx

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when you say large changes above, what Jon did on file is the largest change one can do to a reef tank. Not anything they could do would be a larger systemic change than that action
I think the TV show Tanked does something similar? I've seen many threads where people move tanks to new homes. Nothing about that thread you show is unique to me? Unless I am missing something.

I know I did a 100% water change on live rock 6 times before transferring them to the tank. Everytime I add new coral, they go through a 100% water change.

I suppose overall, i'm lost with whatever is trying to be sold here.
 

brandon429

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Tanked does measure very well the ability to handle mass fish/ammonia in quick cycling. Above Im reading how they measure the addition of new rocks/biota in the tank, its handy to see just a polar opposite action/the total ripping of the biome out, then track how that impacts the overall thing reefers want: a sharp looking tank producing coral with no invasions.

Im not sure bacterial changes matter to us collectively all that much as long as we maintain sharp reefs and good coral production. Its neat just to assemble the spectrum of possible reef care and measure them all. knowing how to influence bacteria sure might reduce our work loads one day, effecting a rip clean sure is a lot of work and cost regarding all new saltwater.
 
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brandon429

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I totally get that. when he first mentions large changes, I was thinking along the lines of putting the reef through a washing machine lol but its adding live rock to live rock and measuring if Im not mistaken, will go back and re read to see if thats the case.

those actions really do affect the biome, live rock per average is six football fields of surface area if its tonga branch/guesstimating, a little rock is truly a lot of bac. thats why we get away with insulting an entire reef while ONLY caring for its rock, is a testament to how influential live rock is in a reef tank. the surrounding surface area doesnt matter much/bold claim/but we can track it above visually in Jon's tank. we took a massive amount of surface area his whole tank was adapted to, and removed about as much as you could instantly remove and still introduced the exact same bioload back. a darn good rebound test in my opinion.
 
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reeferfoxx

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I totally get that. when he first mentions large changes, I was thinking along the lines of putting the reef through a washing machine lol but its adding live rock to live rock and measuring if Im not mistaken, will go back and re read to see if thats the case.

those actions really do affect the biome, live rock per average is six football fields of surface area if its tonga branch/guesstimating, a little rock is truly a lot of bac. that we get away with insulting an entire reef and ONLY caring for its rock, is a testament to how influential live rock is in a reef tank.
Ok. My only take away from all of this is proving/providing actually proof that live ocean rock is better than using dry rock. Likewise, the addition of live sand or mud amplifies microbial communities. To me, this is a no brainer. What is getting me confused though, are all the successful tanks only using dry rock with/or without knowledge of diversifying microbial communities.
 

brandon429

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I keep trying to envision where this measurement leads, what do we do with it

potentials:

-to sell us things; either the actual measure action itself of the resulting doser, or both.
-to increase efficiency of running. backflushing is a staple in the aquatic/marine production industry, reducing that waste and work and expenditure w be beneficial. if your surface area self-unclogs due to bac you can dose, you dont have to backflush
-changes in feed/mass production and waste efficiency ratios, the enduring measure of an efficient biosystem. perhaps measuring changes and knowing exactly which kind of bac endure/select against allows us to get more production out of less feed input, somehow
-whoever pinpoints the bacteria that outcompete dinos wins one million dollars justifiably. be taking samples from dino tanks, before and after successful restoration~
 
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Samina

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Help me out here... What is interesting? I'm not trying to troll.
No worries. I can only speak for myself. But I think there is much we can all learn from this. We all know about the chemistry within our systems and how important their stability is in that regard along with proper lighting and flow. But we are just now scratching the surface on the biome of our systems. Now stability can be talked about in relation to the biome and what effect that stability/diversity has or does not have. Also begs the questions to figure out if having a certain type of diversity within our system is more beneficial than another type.

The diversity of the biome within the home aquaria is regulated by out-competing, natural selection, etc. - and now also shown to be a result from our actions. Something to consider in this. So many folks talk about how when they have been away or have had their “hands” out of the tank for an extended time, the life within it seems generally healthier and happier. I would consider these “hands” to also be the constant tinkering and tweaking some of us do with our systems. Although anecdotal, something to consider. What I find interesting in this is that it’s a step in the direction of providing information to find whether the various types of bacterial families, and the makeup of the systems biome may have an effect on the general health of the system. Obviously, no two independent systems are the same. Another big question, from my opinion, goes to learning and discovering how this stability and various profiles of diversified biomes relate/compare to what we perceive as troubled systems. Systems in which cyano or dinos proliferate.
 

reeferfoxx

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-whoever pinpoints the bacteria that outcompete dinos wins one million dollars justifiably.
Its the human "bacteria" that outcompetes dinos if done correctly ;Hilarious Jokes aside, I suppose that's something to look forward to.
 
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lexinverts

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Ok. My only take away from all of this is proving/providing actually proof that live ocean rock is better than using dry rock. Likewise, the addition of live sand or mud amplifies microbial communities. To me, this is a no brainer.
To better understand the utility of measuring the microbiome of a saltwater aquarium and what it means for aqaurists, you should check out some of the brief articles on Aquabiomics' website.


In my view, having a diverse and appropriate microbial community in our reef tanks makes it less likely that we will have trouble with outbreaks of nuisance algae and harmful bacteria. I base this on the general importance of competition in wide ranging biological communities for keeping one or more species from dominating. We all know what can happen when dinoflagellates dominate the microbial communities in our tanks.

This paper is interesting because it shows that regular maintenance can have a substantial impact on the microbiome in our tanks. In my own experience, I have seen outbreaks of pest algae come right after a water change, etc... Perhaps this research will help us learn why.

What is getting me confused though, are all the successful tanks only using dry rock with/or without knowledge of diversifying microbial communities.
Yes, some people do have great success when starting tanks with bottled bacteria and dry rock, but threads like the one below are testament to how many people struggle with maintaining a balanced microbial community in their reef tanks.

 

reeferfoxx

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Yes, some people do have great success when starting tanks with bottled bacteria and dry rock, but threads like the one below are testament to how many people struggle with maintaining a balanced microbial community in their reef tanks.
I've contributed a lot of my time in the dino threads. The thought of it gives me anxiety. In all my time helping other's, there was never a case where dinos just pop up out of nowhere. expect for rev's tank. Still a mystery to me. As you know they are seeded and then its typically human error that creates infestations. Then it's dependant on the specie and its trigger (ie temp, salinity, nutrient, lighting (maybe), etc)

My own experiences with a dry rock tank has been somewhat documented through the dino thread, my chysophyte thread, and my insane cyano troubles. The tank ultimately failed when i didn't have time for it due to a family crisis.

I appreciate the fact that we are tying to learn about our artificial biomes but i have a hard time believing it will equate to much within the hobby. Especially if the simple answer is seeding diversity.
 
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AquaBiomics

AquaBiomics

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Measuring what, boss?
Sometimes in my attempts at brevity I leave important things unsaid, my apologies for any lack of clarity.

The authors demonstrate (as others have) that what we do to our tanks can have lasting effects on the microbial community. They emphasize that we don't fully understand the functional consequences of these different states. They emphasize that we need to measure these effects, and that aquariums are ideal scenarios for testing many of these things because these are controllable artificial ecosystems in a box.

So I was saying that these authors did a lot with only two aquariums. We (collectively, as a hobbyist community) have a lot more tanks at our disposal. Now that microbiome testing is readily available to the hobbyist, we stand to learn a lot by systematically measuring the effects of various practices (e.g. dosing with mystery product X) on our tanks, along with measuring their effects on the microbiome.

Is that clearer?
 
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AquaBiomics

AquaBiomics

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And I'll add an open question, in a further attempt to clarify my goals with this thread.

As a community, what are the effects of microbial communities that we should be measuring? Here are the ones I've thought about (and measured in some cases).
  • nitrifying activities
  • tendency to grow nuisance algae
  • coral tissue necrosis

What other effects have been attributed by hobbyists to microbes (usually without evidence, since evidence has previously been hard to come by)?
 

lexinverts

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And I'll add an open question, in a further attempt to clarify my goals with this thread.

As a community, what are the effects of microbial communities that we should be measuring? Here are the ones I've thought about (and measured in some cases).
  • nitrifying activities
  • tendency to grow nuisance algae
  • coral tissue necrosis

What other effects have been attributed by hobbyists to microbes (usually without evidence, since evidence has previously been hard to come by)?
Fish health. Some keepers of sensitive, wild caught fish, swear that younger tanks (usually those that are set up with dry rock and bottled bacteria) tend to be really hard on sensitive species. Some of the angel breeders, for example, would never put their breeders in a younger tank, even if the nitrifying community has been clearly established. There may be an effect of the microbiome on the vibrio community in a way that impacts fish health, similar to how we think it might impact coral health.
 
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AquaBiomics

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Fish health. Some keepers of sensitive, wild caught fish, swear that younger tanks (usually those that are set up with dry rock and bottled bacteria) tend to be really hard on sensitive species. Some of the angel breeders, for example, would never put their breeders in a younger tank, even if the nitrifying community has been clearly established. There may be an effect of the microbiome on the vibrio community in a way that impacts fish health, similar to how we think it might impact coral health.
Interesting. I wonder, what is a feasible model system for sensitive wild caught fish?
 

lexinverts

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Interesting. I wonder, what is a feasible model system for sensitive wild caught fish?
My experience was with Pomacanthus.
Perhaps some dwarf angels or butterflies would work.
Singapore angels (Chaetodontoplus mesoleucus) are inexpensive and have a reputation for being touchy.
 
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