Establishing a Healthy Microbiome in a New Aquarium Using Live Rock

[Timfish]

Good to see discussion on microbiomes! I think it needs to be pointed out reef systems have multiple and constantly changing microbiomes. At each taxonomic level the microbiome is being manipulated by the macrobiome species present (1, 2, 3) so the microbiome detected with 16S testing in the water in our reef systems is to a certain degree determined by the types of animals present. We also know coral holobionts are species specific (4, 5) and looking at genotype specifc response to pathogens (6, 7) it seems reasonable the holobiont is also genotype specific. Veron's books on coral distribution show some corals are found in a wide range of environmental conditions and with other species (Montipora digitata or Acropora youngii for example) while some are only found in very specific environmental conditions and/or only in association with other corals of the same genus (like Acropora microclades aka Strawberry Shortcake, 8). Building a data base with 16S testing I think is going to be a huge help in determining what we need to do to keep corals for their normal life expectancies.

1, https://www.ncbi.nlm.nih.gov/pubmed/28828261

2, https://www.ncbi.nlm.nih.gov/pubmed/23303369

3, https://www.ncbi.nlm.nih.gov/pubmed/23882445

4, https://www.int-res.com/abstracts/meps/v243/p1-10/

5, https://2015-mbio322.blogspot.com/2017/11/predatory-bacteriathe-gate-keepers-of.html,

6, https://www.nature.com/articles/s41598-017-02685-1

7, https://nsuworks.nova.edu/occ_stuetd/467/

8, https://reefbuilders.com/2019/06/24/you-wont-believe-where-strawberry-shortcake-acros-live/

 

[hart24601]

I agree that one of the live rock sources was not an improvement over the dry rock in terms of the uglies, but to be clear, both live rock sources had much higher diversity (comparable to a typical reef tank) while dry rock had low diversity.

Also, both live rock sources established effective biological filters while dry rock alone did not.

In other words, both sources of live rock were measurably better than dry rock, but one was much better than the other. I think this is the next step for us to focus on: what makes good live rock vs bad live rock? (And note that I havent even tested the wet dry rock sold by many LFS as "live rock", which I expect will be barely better than dry rock). Both the of the live rock sources I tested here came from the ocean.

I think anyone would be shocked if dry rock produced the diversity of rock from the ocean, particularly over a few months with fairly limited inputs, however it’s good to see your testing showed that difference - if it didn’t I think more questions would be raised about the sampling and testing process not being accurate since it seems pretty obvious the diversity should be higher and it should take much longer to cycle. So that’s great to see!

I just want to caution people reading to not over interpret the results. We get caught up already in chasing numbers, clearly we are most interested in how the tank is operating and the overall health and appearance- if anything I am surprised the LR wasn’t more of a ‘slam dunk’ since the one group appeared to be high quality directly from the ocean but in the tanks phenotype did not produce better results than dry - it also shows that we are not quite ready to say what is good, since this indicates the population components seemingly play a larger role than the overall diversity when it comes to reducing the initial ‘uglies’ which is an easy way to describe the appearance but there can be complex interactions driving that appearance.

 

[Belgian Anthias]

Very important for the coral holobiont seems to be organic carbon. It seems corals are able to manage their own nutrient supply by providing more or less organic carbon, phosphorus and other essential nutrients to its holobiont by releasing mucus, this way regulating growth rates within the holobiont and its own nutrient supply by controlling the food supply and consumption in the coral's microbiome. Of course, this is only possible in an organic carbon limited environment, an oligotrophic environment with minimal but constant nutrient supply.

I doubt if adding so-called "live rock" will improve the coral's microbiome as one only imports competitors with no relation to the coral at all. The coral microbiome, the holobiont, is specific for each coral, contains specific strains, and comes with the coral.

ref: my article in the Makazi Baharini wiki http://www.baharini.eu/baharini/doku.php?id=nl:makazi:theorie:koraal_holoboint

 

[VR28man]

Thanks for the input. I’m most likely going to use TBS again or possibly see what kind of coral live rock is out there depending. What I love about TBS is all the great stuff you get and with not much die off since he ships them in water submerged!

Indeed, one of the reasons I'll go with them when I get my next tank.

And note that I havent even tested the wet dry rock sold by many LFS as "live rock", which I expect will be barely better than dry rock

I would be very interested in that too. My impression is that the various "wet dry rock" ("Real Reef", Caribsea Life Rock, normal Walt Smith 2.1) is basically various kinds of artificial rock seeded with some kind of spore form of nitrifiying bacteria, so when it gets into salt water they'll start growing out a few selected species.

 

[AquaBiomics]

Very important for the coral holobiont seems to be organic carbon. It seems corals are able to manage their own nutrient supply by providing more or less organic carbon, phosphorus and other essential nutrients to its holobiont by releasing mucus, this way regulating growth rates within the holobiont and its own nutrient supply by controlling the food supply and consumption in the coral's microbiome. Of course, this is only possible in an organic carbon limited environment, an oligotrophic environment with minimal but constant nutrient supply.

I doubt if adding so-called "live rock" will improve the coral's microbiome as one only imports competitors with no relation to the coral at all. The coral microbiome, the holobiont, is specific for each coral, contains specific strains, and comes with the coral.

ref: my article in the Makazi Baharini wiki http://www.baharini.eu/baharini/doku.php?id=nl:makazi:theorie:koraal_holoboint

I think you're right to bring up the coral holobiont. The corals that we add to our tanks house specific communities of microbes that are important for the corals. So I think we can agree live rock is not needed to provide the coral symbionts.

But that is only one subset of the microbial community in an aquarium, right? In fact, when most people add live rock I think they aren't aiming to improve the coral microbiome, they're primarily going for a functional biofilter. Thats not about the coral microbiome, its more about the right community of microbes in the sediments and pores of rocks. (Although I concede that in a mature tank stocked with large colonies of corals, a large fraction of the ammonia is probably processed through the coral holobiont rather than the sediments)

Thats just one aspect of non-coral related microbial functions. There also appears to be competition between some nuisance algae and some prokaryotes, although the details arent as clearly worked out as with nitrifying microbes.

I suspect the benefits of live rock extend beyond these measurable benefits (nitrification and inhibiting algal growth). These are just the ones I thought to measure. Since I know we have people with more experience using live rock than me, I wonder -- what other benefits are proposed for live rock that could be tested in an experiment like this?

 

[jefra]

Great research. Could the reduced uptake of ammonia by the dry rock have hindered further colonization/diversity? I'd imagine if the bacteria are exposed to a prolonged moderate ammonia concentration, that could negatively affect both the total bacterial population and microbiome diversity. Even though ammonia is metabolized as an energy source, in sufficient concentrations, it's still toxic.

 

[jefra]

Eli - I'd be very interested in finding out which organisms are responsible for keeping the sand bed clear in 'Live Rock-b'.

Right?! Bottle those guys ASAP, I'll preorder it! I love the look of a sandbed, but run a bare bottom tank since nothing I do keeps it clean for long.

 

[AquaBiomics]

Right?! Bottle those guys ASAP, I'll preorder it! I love the look of a sandbed, but run a bare bottom tank since nothing I do keeps it clean for long.

I completely relate to this. I love the way a clean sandbed looks, aesthetically its one of the top priorities for me in a display tank - visible patches of open white sand. But so often I struggle with nuisance algae on my sand. Thats why these effects caught my eye -- I was like wow, I wish the sand in my living room tank looked like the sand in these experimental tanks!

While we all figure out whether and how effects like this could be duplicated with a bottled product, in the meantime... adding additional live rock is looking pretty appealing.

 

[rushbattle]

I completely relate to this. I love the way a clean sandbed looks, aesthetically its one of the top priorities for me in a display tank - visible patches of open white sand. But so often I struggle with nuisance algae on my sand. Thats why these effects caught my eye -- I was like wow, I wish the sand in my living room tank looked like the sand in these experimental tanks!

While we all figure out whether and how effects like this could be duplicated with a bottled product, in the meantime... adding additional live rock is looking pretty appealing.

I posted in the other thread, but I had huge amounts of cyano in my fishless coral system. I added a small piece of live rock from a stock tank I am using to hold some Florida live rock in anticipation of the new systems. Within a week I could see ubiquitous cyano mats starting to shrink and shed whole pieces. It has continued decreasing slowly since then, and while the cyano is not gone, it doesn’t come back much if at all once I siphon it out during a water change, etc. I wish I had tested the biome before so we could measure it now. It was certainly not a fully controlled, replicated and statistically significant study but it would be nice to see what changed in the biome between cyano city before and now.

 

[Belgian Anthias]

I think you're right to bring up the coral holobiont. The corals that we add to our tanks house specific communities of microbes that are important for the corals. So I think we can agree live rock is not needed to provide the coral symbionts.

But that is only one subset of the microbial community in an aquarium, right? In fact, when most people add live rock I think they aren't aiming to improve the coral microbiome, they're primarily going for a functional biofilter. Thats not about the coral microbiome, its more about the right community of microbes in the sediments and pores of rocks. (Although I concede that in a mature tank stocked with large colonies of corals, a large fraction of the ammonia is probably processed through the coral holobiont rather than the sediments)

Thats just one aspect of non-coral related microbial functions. There also appears to be competition between some nuisance algae and some prokaryotes, although the details arent as clearly worked out as with nitrifying microbes.

I suspect the benefits of live rock extend beyond these measurable benefits (nitrification and inhibiting algal growth). These are just the ones I thought to measure. Since I know we have people with more experience using live rock than me, I wonder -- what other benefits are proposeAnd this is easily provedd for live rock that could be tested in an experiment like this?

A closed reef system may be considered to be one big bio-filter.
But in the microbial world, the conditions will be completely different as measured in the water column. Every biofilm will be different in composition and may contain hundreds of different species each having a specific task.
A nitrifying biofilm contains at least 40% micro-organisms using an anaerobic pathway making it possible for the bio biofilm, a microbiome, to function and make it possible to reduce ammonium. All nitrifying biofilms remove nitrogen due to denitrification. For the microbiome and bio-chemics, it will make a big difference on what base and or substrate such a bio- film is growing and of course the surrounding water.
A so-called " live rock" will soon be the same as any other rock in the system.


Are people going for a " functional" biofilter by adding so-called " live rock"? I think most do, but is it a good approach?
For decades people are told they should use "live rock". Why?

Live Rock in the Marine Aquarium

The selection and use of live rock and live sand

chucksaddiction.thefishestate.net

http://www.reefkeeping.com/issues/2004-05/rs/feature/index.php

A simple canister filter used as a bio-filter will function and filter the water many times better compared to a tank filled with " live rock".
Why reefers banned active nutrient management and replaced it with very expensive passive nutrient management and accept the consequences of having a very low max carrying capacity which can not be managed as desired? The specialized fora are full of questions for solving problems caused by the belief so-called " live rock " will do what it is intended to do.

After decades of promotion, there is still not any proof available for so-called "live rock" that may perform better as a bio-filter than any other calcium-carbonate based rock of the same size.
A " functional " biofilter is a filter that makes the nutrient content in the system manageable. An aquarium grows, the bioload will increase. A " functional" biofilter makes it possible to adjust the carrying capacity as needed.
If it is only about microbiome then everything in the tank and the tank itself is a good " functioning" bio-filter.

For a good " functional" bio-filter, one does not need any " live rock". So-called "live rock" has a very low capacity as a biofilter due to the very low water exchange rate and the filter capacity is comparable to any other colonized rock of the same size. If one wants to import microbial diversity no heavy rock is needed. A little bit sand from a seaweed field from the top layer till at least 10cm deep and a little bit of weed and some scrapings from real a live rock ( reef rock) will bring all microbial diversity needed. Maybe It may be sent to the home by express post and be delivered at the home address within 12h to 24h after harvesting. This way a lot more diversity may be introduced as any " cured " so-called "live rock" will be able too.
Someone who is having a refuge with sand and rock started up and seeded this way will have all the diversity needed to seed a reef aquarium without any so-called " live rock"



In nature, corals depend mainly on organic nutrients

 

[jefra]

After decades of promotion, there is still not any proof available for so-called "live rock" that may perform better as a bio-filter than any other calcium-carbonate based rock of the same size.

Bottled bacteria and the various forms of highly porous biological media are relatively new. That’s likely why live rock has been promoted for decades.

I’d argue that this very thread is proof of live rock’s superior filtration ability compared to base rock and other artificial alternatives.

 

[AquaBiomics]

I posted in the other thread, but I had huge amounts of cyano in my fishless coral system. I added a small piece of live rock from a stock tank I am using to hold some Florida live rock in anticipation of the new systems. Within a week I could see ubiquitous cyano mats starting to shrink and shed whole pieces. It has continued decreasing slowly since then, and while the cyano is not gone, it doesn’t come back much if at all once I siphon it out during a water change, etc. I wish I had tested the biome before so we could measure it now. It was certainly not a fully controlled, replicated and statistically significant study but it would be nice to see what changed in the biome between cyano city before and now.

This is great. In the pre-microbiome days I've used a different approach that I suspect had the same underlying mechanism. I've found repeatedly that dosing NO3 helped clear up cyano mats, and I know others have had similar experiences with NO3. Many of us speculate that the reason is adding NO3 allowed other organisms that were nitrate limited to outcompete the cyano for other nutrients (e.g. PO4).

Whether by adding new microbes (as in your experience with live rock) or by adding nutrients to alter the relative growth rates of existing microbes, it appears that cyano problems are especially sensitive to adjustments in the microbiome. Which is sort of self-evident, I guess, when I write it out like that. It makes sense, as cyanobacteria are the only visible members of the microbiome in our tanks...

Its a beautiful thing watching these reddish purple cyano mats shrink, however we achieve it.

 

[AquaBiomics]

A so-called " live rock" will soon be the same as any other rock in the system.

Respectfully, where is the evidence this is so? (I mean, at a microbial level). And what do you mean by "soon"?

I've read similar statements many times, usually flipped around as "dry rock becomes live rock soon after you add it to the tank". Certainly the LFS that sell wet base rock as "live rock" seem to have adopted that meaning

But when I tested this statement, I found it did not describe how microbial communities behaved in my tanks. Live rock rapidly developed a microbial community like that of an established reef tank. Dry rock did not. It remained pretty much a flat line in diversity and showed no evidence of establishing a functional biofilter.

Now if we're getting into how to inoculate the tank with the right microbes, we're basically in the same school of thought as live rock. Whether its sediment or larger pieces of rock, the goal isn't the aragonite, it's the biofilm. (Although I do think there is good reason to believe that deeper chambers within a large porous rock will house different communities than the surface of sand grains, but this is fine tuning the same basic strategy).

Would a tank started with high-quality "live sand" do as well as one started with high-quality live rock? I wouldn't bet much money against that proposition. If I do another batch of tank setup experiments maybe I'll include that. Certainly sounds like a reasonable way of importing the right microbes (although I'm very skeptical of the "live sand" that sits on the shelf at pet store chains, I can imagine your suggestion of real live sand and rubble from an established tank or a reef environment might being very effective. Sadly I am very far from a reef ecosystem but for reefers in the tropics that would be a great thing to try)

 

[brandon429]

TBS has that live sand quality you're looking for, the true kind of sand with wigglers in it. Its the only kind of sand we dont pre-rinse in our sand rinse thread.

 

[Paul B]

For a good " functional" bio-filter, one does not need any " live rock". So-called "live rock" has a very low capacity as a biofilter due to the very low water exchange rate and the filter capacity is comparable to any other colonized rock of the same size.

That's why I have been using a reverse Undergravel filter for the last 45 years. Oxygen runs our tanks and is what most bacteria and other microorganisms require.
Where there is oxygen, there is life and besides the life that we depend on to purify the water, there is life that we depend on to feed our sponges, corals and small fish.

 

[Belgian Anthias]

Respectfully, where is the evidence this is so? (I mean, at a microbial level). And what do you mean by "soon"?

The evidence is everwhere, in each mixed reef aquarium wich uses a mix of base rock and so called "live rock". To cycle a tank one must take at least a few months and it will never be finisched.

I've read similar statements many times, usually flipped around as "dry rock becomes live rock soon after you add it to the tank". Certainly the LFS that sell wet base rock as "live rock" seem to have adopted that meaning

Maybe the "live rock" lobby wants reefers to continue to "believe"? They never tried to prove what is believed, for a good reason. A newly established aquarium will never become a marine aquarium if not seeded with marine bacteria as they are completely different, for a reef aquarium this may be coral specific strains. The big question stil is: do we need rock coming from the other side of the planet to seed a tank? For sure we do not need it for its ability to manage aerobic and anaerobic remineralization.

But when I tested this statement, I found it did not describe how microbial communities behaved in my tanks. Live rock rapidly developed a microbial community like that of an established reef tank. Dry rock did not. It remained pretty much a flat line in diversity and showed no evidence of establishing a functional biofilter.

You compared sterrile rock with "live" rock! What if so-called "live rock" is compared to any wet base rock which has been in an aquarium and may be considered "alive"? You used 3 types of rock of wich no is "real live rock" but 2 of them are sold as " live rock". What if the sterrile rock ( used in marine aquaria since the sixties) was first seeded in an established aquarium? Would there still be any difference? Well, I think the difference will be in favor of the seeded base rock.

Now if we're getting into how to inoculate the tank with the right microbes, we're basically in the same school of thought as live rock. Whether its sediment or larger pieces of rock, the goal isn't the aragonite, it's the biofilm. (Although I do think there is good reason to believe that deeper chambers within a large porous rock will house different communities than the surface of sand grains, but this is fine tuning the same basic strategy).

It is not possible to inoculate a tank with "the right" bacteria as till now specific strains can not be cultivated and certainly will not survive in a bottle. Please define: The "right" bacteria.

Would a tank started with high-quality "live sand" do as well as one started with high-quality live rock? I wouldn't bet much money against that proposition. If I do another batch of tank setup experiments maybe I'll include that. Certainly sounds like a reasonable way of importing the right microbes (although I'm very skeptical of the "live sand" that sits on the shelf at pet store chains, I can imagine your suggestion of real live sand and rubble from an established tank or a reef environment might being very effective. Sadly I am very far from a reef ecosystem but for reefers in the tropics that would be a great thing to try)


Reefers in the tropics tried it since the sixties. The first reef aquaria where so-called " natural systems"
The reef ecosystem is far more complex as one is able to duplicate in captivity, in a closed system. Till now they are not able do it in Lab settings.

Live Rock in the Marine Aquarium

The selection and use of live rock and live sand

chucksaddiction.thefishestate.net

The test is started adding 1ppm of ammonia which will be transformed into ammonium. This means NOB present must survive till most ammonium is used up. NOB is senstive for the presence of ammonia and will only start using nitrite when most ammonia is used up showing a high nitrite level. But also a high nitrite level will inhibit growth. High ammonia levels are also slowing down AOB and archaea. High growth rates are dependable of the C/N ratio and of essential nutrients as phosphate availability. Sterile rock can not support growth and NOB can only be introduced after most ammonia is reduced. There has been done a lot of research concerning the issue of biological filtration
My opinion you have tested something very predictable due to the setup.

Of course, adding some "real" fresh rock straight from the sea will be beneficial for the development of diversity in a new set up tank. No doubt about that.

I am not a believer in the " live rock myth" and in my opinion, such a test needs another setup.

The Parable of the Bacteria in a Bottle

 

[Belgian Anthias]

Bottled bacteria and the various forms of highly porous biological media are relatively new. That’s likely why live rock has been promoted for decades.

I’d argue that this very thread is proof of live rock’s superior filtration ability compared to base rock and other artificial alternatives.

We used highly porous rock in our first marine aquarium setup in 1972. Do you mean bio-polymers? For the moment bio-polymers are tested to remove micropollutants and by which one can program the max size. This gives the possibility to remove small DOC but leave bigger particles for feeding filter-feeders. The end of the skimmer?
High porous rock was subject of a lot of research, meanly as an absorber but also used as a bio-filter. There is not much which is not known about GAC. It is still a passive filter method and the nitrogen removal rate is very low due to the low and variable water exchange rate . It may be more effective and more easy to remove 20% at a high flow rate as 100% at a very low flow rate.
Bacteria in a bottle? What is in the bottle?
The Parable of the Bacteria in a Bottle

Live rock was promoted once to replace a simple bio. The result is a low carrying capacity unable to manage.

 

[AquaBiomics]

You compared sterrile rock with "live" rock! What if so-called "live rock" is compared to any wet base rock which has been in an aquarium and may be considered "alive"? You used 3 types of rock of wich no is "real live rock" but 2 of them are sold as " live rock". What if the sterrile rock ( used in marine aquaria since the sixties) was first seeded in an established aquarium? Would there still be any difference? Well, I think the difference will be in favor of the seeded base rock.

Respectfully, I think you may have misread something. I used two sources of actual live rock (from the ocean). And one source of dry base rock, which as far as I can tell is exactly what youre advocating.

And the evidence very clearly showed that live rock produced a diverse microbial community similar to the community in an established aquarium, while the dry rock did not. The results weren't hard to see. They were pretty dramatic, in favor of the live rock.

Again, where is the evidence (data on microbial communities) that dry rock becomes live rock when placed in water? I tested that statement and found it to be incorrect. Has someone else conduced an experiment with different results?

Or are you perhaps relying on assumptions about what microbes "must be there"?

It is not possible to inoculate a tank with "the right" bacteria as till now specific strains can not be cultivated and certainly will not survive in a bottle. Please define: The "right" bacteria.

I just showed that you can absolutely inoculate a tank with the right bacteria, as reefers have known for decades. Using Live Rock.

With that said, I tend to agree with you about bacteria in a bottle. Wait til my next article comparing dry rock with dry rock plus bacteria in a bottle

What are the right microbes? That is a great question, and we don't know the complete answer. But as a starting point I suggest this: the bacterial community in a mature, thriving reef tank has the right microbes.

The community in a mature reef tank is profoundly different than that in a tank full of wet base rock. But a newly established live rock tank is diverse and similar to an established tank. This is what the evidence shows.

I am not a believer in the " live rock myth" and in my opinion, such a test needs another setup.

I'm afraid that from where I'm standing, it appears you are not a believer in the live rock data. I'm not advocating blindly following myths here, but there is pretty clear evidence that live rock produces a diverse community similar to an established aquarium, while dry rock does not. Do you have evidence to the contrary? I would be curious to read it.

 

[reefwiser]

Many timeS hobbyist confuse the microbiome bacteria with nitrifying bacteria.
while bacteria from a Bottle will seed nitrifying bacteria it will not seed the microbiome bacteria. I learned this back in the 80’s when I first used “Live” rock form the ocean. I had great success with the live rock that I didn’t with dry rock. It was due to the microbiome from the ocean.

 

[X-37B]

Very informative article! I started my 120 with 30lbs established real live rock when I broke down my smaller tank. I mixed it with 30lbs carib sea colored rock. Tank is now approching 6 months.
My observations: the caribsea man made rock had the uglies for about 3 months. The live rock did not.
Currently the caribsea rock is devoid of the ugly algae and is being covered in coralinne. So is the bottom and back glass.
Virtually no cycle to speak of.
Started adding coral @ 1.5 months.
Currently 9 fish couple shrimp various snails and 40+ corals of various sizes all growing.
Several people I know are still fighting the uglies at 6 month. They started with dead white rock. The few who added 1 or 2 pieces of live rock have gone behond the ugly stage much quicker.
There is observational proof that live rock helps. I do dose 10ml of mb7 every couple of weeks but thats it.
Where I live the lfs only carry dead rock. I aquired mine about 3 years ago before the ban.
Keep up the testing and thanks.