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

Nano sapiens

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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)?
Denitrification
Metabolization of coral allelopathic substances
 
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AquaBiomics

AquaBiomics

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Denitrification
Metabolization of coral allelopathic substances
You aim right for the Interesting and Difficult! Very cool, I had honestly not thought about the second one at all.

Denitrification is such a challenge in my mind - in terms of measuring the function, how do we distinguish between uptake of nitrate by phototrophic organisms (even at night) versus denitrification, in a whole aquarium setting?

Removal of coral allelopathic substances -- I wonder how can we measure such a thing? Do you have experience with specific sources (I know soft corals are generally blamed) or victims?
 
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AquaBiomics

AquaBiomics

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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.
I havent followed this specific case. Lets clarify the question so we can make sure to sample it appropriately. Is your proposition that the community will return following a rip clean? (I am assuming rip clean means 100% water change with cleaning of sediment and rocks?)

If that were the question, it seems to me that at minimum we would want to sample before the cleaning, shortly afterwards, and at some later time. Right?

Let me know if I misunderstood the question to be tested. I'd be very interested in testing a case like that, it's relevant for immediate decisions faced by aquarists and can be tested in a relatively short time scale (~1-2 months).
 

brandon429

why did you put a reef in that
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Agree fully thats what I hope to know from aggressively cleaned systems once you can measure them microbially. In fact we are on the fifth year of doing this across hundreds of reefs in the sand rinse thread, we already know the systems and corals respond well or they’d have drummed me out of town but we do not know how much we are changing the biota or how long that lasts or how the corals which depend on stasis tolerate our insults. They’re happy though. The rip cleans pale in comparison to a decent storm in nature most likely ~ adapted


just on the macro level/seen from full tank shots all rip cleaned aquariums have the best brightest polyp extension. we have no outliers in the thread, and the best I can liken it to is the backflushing of a large filter system; to use force to dislodge and unclog pores, ejecting mixed general aerobes + organic stores still leaves a base community in place or all these tanks would recycle and die. The renewed surface area is more active in every beneficial way vs when it was clogged, and now the systems are hungry for renewed feeding and we take advantage of that and proceed to fill it all right back up with waste again... it’s the circular price of having sand in my opinion. We refuse to allow eutrophication takeover. Jon was the first id ever seen do the job preventatively, 99% of our work is in reaction to an invasion or an upcoming home move



we have identified detritus, particulate organic matter, as the sole cause of old tank syndrome (managing detritus makes a no lifespan limit reef tank) and the sole risk to an aquarium that must be relocated or deep cleaned for some reason or another.

we show the irony of deep cleaning imparting permanent self regulation to the system microbially. Flush out mud, biofilter lasts forever and doesn’t require recharging * unless there are strains we could be adding to never have to rip clean in the first place!
 
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brandon429

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Though we cannot see bacteria in that work thread, it’s inferred from the thread patterns that the old claim of remove sand slowly so rocks can take on more bac is a fallacy

the leftover rocks are either enough surface area by themselves or they’re not; what happens to the sand doesn’t matter.

****you have shown it matters to biome distribution, no doubt*** but we are saying it doesn’t matter practically. The public only cares if their corals fish and rocks continue working great after our sandbed insults.

surfaces regulate the degree of bac they support by water shear, inter space competition and feed avail among others but removing one portion of surface area (sand) doesn’t mean the live rock must take on its replacement bac. It means the live rock alone by itself manages its ammonia-controlling bac independently from the sand, thats why any degree of decent live rock will instantly handle the full bioload from a tank that used to have sand surface area but was removed all at once.


we take several systems there above and rip out the whole sandbed and not put one back. The liverock instantly had to take over, it does in each case and Daniel was able to measure the event with a mindstream ammonia meter, no spikes. All fish and fish feed was managed by rock alone, what we do to sandbeds isn’t mattering as long as it’s thorough—-we are treating sandbeds horribly in that thread and results are great.
 
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Nano sapiens

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You aim right for the Interesting and Difficult! Very cool, I had honestly not thought about the second one at all.

Denitrification is such a challenge in my mind - in terms of measuring the function, how do we distinguish between uptake of nitrate by phototrophic organisms (even at night) versus denitrification, in a whole aquarium setting?
I agree that this is a tall order, but how about something like this...

To determine the relative denitrification of these two pathways in a 'typical' healthy reef aquarium system (once the overall rate of denitrification in such a system is first determined), would require the removal of as many of the phototrophic macro organisms as feasible from the system. Once completed, then the remaining denitrification would be accomplished primarily by the microorganisms. Keeping all other parameters (especially feeding) constant, then the difference between the denitrification rate of the whole system minus the denitrification rate of just the micro organisms would give the rate of denitrification of the phototrophic organisms. This could provide a general baseline determining which of the two groups actually contributes more to a 'typical' reef system's denitrification.

Removal of the phototrophic macro organisms from a typical reef aquarium is a hurdle. But a reef aquarium pre set up with holes drilled in the live rock, and all the phototrophic organisms on frag plugs, would perhaps be the easiest way to allow removal.

Removal of coral allelopathic substances -- I wonder how can we measure such a thing? Do you have experience with specific sources (I know soft corals are generally blamed) or victims?
Soft corals and gorgonians are the most well known families that produce allelopathic substances. But many stony corals are now known to have their own allelopathic substances, too. When one considers that many successful fully stocked 'mixed reef' systems with potentially toxic species thrive with little, or even no chemical filtration, something quite extraordinary is going on. Some authors have hypothesized that the corals 'get used to their nasty neighbors' (habituation), others that the allelopathic substances are neutralized by 'something' in the system. Thought is, could that 'something' be bacteria that utilize the allelopathic chemicals as an energy source?

To prove something like this would require two aquarium setups, one with a full robust microbiome and one sterile. Place a few coral species together (but not physically touching) that are known to be toxic/don't have resistance to the other's toxin in both setups and observe the results.

Ralph.
 
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AquaBiomics

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I agree that this is a tall order, but how about something like this...

To determine the relative denitrification of these two pathways in a 'typical' healthy reef aquarium system (once the overall rate of denitrification in such a system is first determined), would require the removal of as many of the phototrophic macro organisms as feasible from the system. Once completed, then the remaining denitrification would be accomplished primarily by the microorganisms. Keeping all other parameters (especially feeding) constant, then the difference between the denitrification rate of the whole system minus the denitrification rate of just the micro organisms would give the rate of denitrification of the phototrophic organisms. This could provide a general baseline determining which of the two groups actually contributes more to a 'typical' reef system's denitrification.

Removal of the phototrophic macro organisms from a typical reef aquarium is a hurdle. But a reef aquarium pre set up with holes drilled in the live rock, and all the phototrophic organisms on frag plugs, would perhaps be the easiest way to allow removal.



Soft corals and gorgonians are the most well known families that produce allelopathic substances. But many stony corals are now known to have their own allelopathic substances, too. When one considers that many successful fully stocked 'mixed reef' systems with potentially toxic species thrive with little, or even no chemical filtration, something quite extraordinary is going on. Some authors have hypothesized that the corals 'get used to their nasty neighbors' (habituation), others that the allelopathic substances are neutralized by 'something' in the system. Thought is, could that 'something' be bacteria that utilize the allelopathic chemicals as an energy source?

To prove something like this would require two aquarium setups, one with a full robust microbiome and one sterile. Place a few coral species together (but not physically touching) that are known to be toxic/don't have resistance to the other's toxin in both setups and observe the results.

Ralph.
Interesting ideas, thanks for expanding on them.

I hadnt thought much about the coral allelopathy very much, but thats an interesting one to explore. We could start with the question: Many reefers have documented allelopathic effects of certain corals on other corals, suggesting they are producing large amounts of biologically active compounds. How does the presence of a coral with strong allelopathic effects affect the microbiome?

(Although I've run several mixed reefs I have never tested for these effects and havent observed these effects myself).

I've mostly heard about these effects from "leather" type soft corals, which is a pretty broad group. Anyone have recommendations which corals have the strongest allelopathic effects?
 

fermentedhiker

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allelopathy is a complex subject unto itself. From my freshwater planted tank days vascular plants engage in allelopathic warfare against microalgae. I seem to remember reading that ulva exudes something that inhibits dinos awhile back. To further complicate the question something from my beekeeping days comes to mind. Bees suffer from various pathogens (viral, fungal, bacterial) some of which compete with one another. For example pathogen A might inhibit pathogen B, which in turn inhibits pathogen C, which comes full circle and inhibits pathogen A. The interactions are so numerous and interconnected I'm not sure how one would go about formulating an experiment that would provide meaningful data.
 

Nano sapiens

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Interesting ideas, thanks for expanding on them.

I hadnt thought much about the coral allelopathy very much, but thats an interesting one to explore. We could start with the question: Many reefers have documented allelopathic effects of certain corals on other corals, suggesting they are producing large amounts of biologically active compounds. How does the presence of a coral with strong allelopathic effects affect the microbiome?

(Although I've run several mixed reefs I have never tested for these effects and havent observed these effects myself).

I've mostly heard about these effects from "leather" type soft corals, which is a pretty broad group. Anyone have recommendations which corals have the strongest allelopathic effects?
Borneman's 'Aquarium Corals' has a section on pg 111 describing 'Patterns of General Toxicity in Some Soft Corals'. Regularly highly toxic: Sarcophyton, Lobophyton and Lemnalia. Variably highly toxic: Cladiella, Paralemnalia, Sinularia, Heteroxenia, Nephthea, Efllatounaria, , Cespitularia. Occasionally highly toxic: Xenia, Briareum, Dendronephthea. Rarely highly toxic: Anthelia, Capnella
 

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