Establishing a Healthy Microbiome in a New Aquarium Using Live Rock

[SDK]

Thank you for adding some well thought out hard data to this ongoing debate.

I have always gone to great lengths to start tanks with good live rock from multiple sources. My observations over the years absolutely correlate with your experiment.

One thing I would like to see is data on a tank started with all dry rock and some of the additives like Bio Spira or Dr Tims. Only because this seems to be a very common practice vs. just using dry rock and an ammonia source at startup.

I am looking forward to the upcoming installments on this...

 

[brandon429]

Dinoflagellate work threads by mcarroll and taricha are out to combined 200+ pages nowadays and they use the competitive method to earn results (intentionally boosting tank diversity, uglies sometimes, to quell invasive dinos)


In 200+ pages of patterning, they both pointed out early on that live rock was beating dry rock substantially in having fewest dino issues and your tests really drill that down into specifics

The measured communities above set off the chain of events and support that allow eventual benthic communities to eat or suppress chemically or physically today's top reef tank scourge.

 

[AquaBiomics]

Eli - I'd be very interested in finding out which organisms are responsible for keeping the sand bed clear in 'Live Rock-b'. Even well established reef tanks can be afflicted with the rust-colored organism seen in the first two photos , especially after some type of major disturbance (I've battled this a few times in 11 years of running a nano and still have a light dose of it now). I wonder if it is a type of cyanobacteria, perhaps, that is out competed by specific bacteria and/or archaea? Or simply that the tank with Live-Rock-B is better at processing nutrients since it has many more abundant nutrient processing microbes driving nutrients low enough to inhibit growth of the sand bed organism? Thoughts?

Great question, I wish I had the answer. After watching these tanks for several months I've concluded that a detailed study of the succession of algal and microbial types is needed. It really looks like an ecology textbook example of succession, with multiple waves of different colored algae. I'm thinking about restarting a few tanks early in the new year, sampling them frequently (maybe 2 times a week) and using sequencing to identify both the algal communities and the microbial communities.

You bring up one good possibility, competition for nutrients. I find this plausible. Certainly dry vs live-b had a big difference in nutrient processing.

But live-a also had a nitrifying community, just at lower levels. And it looks just like the dry rock in terms of the uglies (still does, at about 8 months). This makes me suspect there is more to it than just nutrients.

Marine biofilms play important roles in determining what settles on a surface, ranging from promoting settlement of some organisms, to inhibiting settlement of others. Some microbes in these communities even feed on the algae, a more direct form of competition.

Some combination of these is probably driving the patterns in these tanks. I'm looking forward to adding algal IDs to the story so we can discuss it in more detail than brown dust or red slimy stuff. Because at a visual level thats about the best I can do!

 

[i_am_mclovin]

Since this material came from a wholesaler, even if I shared specific contact details the best way to get it would still be the same - ask your LFS if one of their wholesalers carries nano branch rock from Tonga.

Of course, I can offer no guarantee the rock you get has the same microbiome. I don't have any inside info about the supply chains for this stuff. (With that said, I am currently seeking some to add to my own home tanks, following the same strategy I suggested above. Its the one I know was good, so I cant resist trying it again!)

I have the ability to get stuff wholesale, so that helps thank you! I'll have to see who still has some Tonga live rock. I think the most important note I saw is that it's natural live rock not man made cultured live rock. I have used some of the best cultured stuff including from TBS and while it is completely amazing, that is the one complaint I had is that the "ugly" you get in algae etc sucks. It is interesting that this possibly is coming due to something that is in the cultured/man made rock.

 

[Lowell Lemon]

Not at all surprised by the results of this study. This mirrors the actual experience with the use of quality live rock in aquarium use for over 30 years as a hobbiest, manufacturer of reef aquariums and equipment. Without quality live rock it is a struggle to establish solid aquarium communities.

Quality live rock is the most important factor in success with reef tanks in my experience. There I said it.

Great study and good science.

 

[Timfish]

First of all I want to say how excited I am to finally see 16S testing made available to aquarists!!!!

It is really great to see some science showing the benefits of live rock! Delbeck and Sprung as well as Nilsen and Fossa both touted the importance of live rock in their books but unfortunately fear mongers hyping the risks of unwanted hitchhikers and ignoring the benefits swayed many hobbyests.

Over 2 decades ago I had a very brief conversation with a director of a hospital's infectious disease department about bacteria that was significant in changing my approach to reef keeping. Even though testing for bacteria was not an option at the time, I started thinking about reef systems holisticly. While this didn't sit well sometimes with a client sometimes, the system was more important than fixing a problem with a fish or with a coral. I started avoiding doing things if there was potential risk to altering a systems bacteria. I also started using water from healthy tanks to help remidiate systems I was having problems with. It was also quickly obvious there was a lot more going on than simply PO4 and NH4/NO3 issues as there did not seem to be much correlation between them and coral or nuisance algae issues.

Trying to stay abreast of current research it's been fascinating to see the concept of the coral holobiont develop. Additionally the science showing how the various forms of DOC being produced in our systems by algae and corals is influencing the types of bacteria and how the types of bacteria being promoted is in turn affecting our corals. (For those interested Forest ROhwer's "Coral Reefs in the Microbial Seas" is an excellent introduction to the roles of DOC and bacteria to healthy reef ecosystems.) Finally being able to do 16S testing for bacterial variables that directly influence the health of our systems and corals is going to be a real eye opener!

I have a question about the two types of live rock you used. Did you see any difference in the type or amount of sponges between Live A and Live B? I ask because Haas, et al,¹ ² ³ has shown DOC released by corals and especially labile DOC released by algae influences the types of bacteria and de Goeij ⁴ has shown cryptic sponges remove labile DOC roughly a thousand times faster than bacterioplankton (30 min. vs 20 days). Could the differences you documented between Live A and Live B possibly be attributed to cryptic sponges?


1. https://peerj.com/articles/108/?utm_source=TrendMD&utm_campaign=PeerJ_TrendMD_0&utm_medium=TrendMD

2. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027973

3. https://www.nature.com/articles/nmicrobiol201642

4. https://www.rug.nl/research/portal/files/14555035/13completethesis.pdf (Ch. 3 pg. 50 1st paragraph)

 

[VR28man]

Excellent post and thread, @AquaBiomics confirming (and adding details explianing) old time experience, and honestly just plain common sense.

So asking the obvious question, where can one obtain live rock B?

i’d recommend aquacultured rock from Florida.

From @liverock:

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!!! THIS IS A DEMO SITE – CONTACT US AT [email protected] TO PLACE AN ORDER !!! We are working to get the site rocking and rolling soon! The “Package” the perfect combination of Live Rock, Live Sand, and Critters to create a mini ocean in your tank SHOP The “PACKAGE” LIVE SAND SHOP LIVE...

www.tbsaltwater.com

or an excellent vendor in the keys:

Aquarium Aquacultured Live Rock Supplier Archives

Are you looking to add some more authenticity to your aquarium? Contact KP Aquatics who offers aquarium aquacultured live rock to give it a unique style!

www.kpaquatics.com

 

[AquaBiomics]

First of all I want to say how excited I am to finally see 16S testing made available to aquarists!!!!

It is really great to see some science showing the benefits of live rock! Delbeck and Sprung as well as Nilsen and Fossa both touted the importance of live rock in their books but unfortunately fear mongers hyping the risks of unwanted hitchhikers and ignoring the benefits swayed many hobbyests.

Over 2 decades ago I had a very brief conversation with a director of a hospital's infectious disease department about bacteria that was significant in changing my approach to reef keeping. Even though testing for bacteria was not an option at the time, I started thinking about reef systems holisticly. While this didn't sit well sometimes with a client sometimes, the system was more important than fixing a problem with a fish or with a coral. I started avoiding doing things if there was potential risk to altering a systems bacteria. I also started using water from healthy tanks to help remidiate systems I was having problems with. It was also quickly obvious there was a lot more going on than simply PO4 and NH3 issues as there did not seem to be much correlation between them and coral or nuisance algae issues.

Trying to stay abreast of current research it's been fascinating to see the concept of the coral holobiont develop. Additionally the science showing how the various forms of DOC being produced in our systems by algae and corals is influencing the types of bacteria and how the types of bacteria being promoted is in turn affecting our corals. (For those interested Forest ROhwer's "Coral Reefs in the Microbial Seas" is an excellent introduction to the roles of DOC and bacteria to healthy reef ecosystems.) Finally being able to do 16S testing for bacterial variables that directly influence the health of our systems and corals is going to be a real eye opener!

I have a question about the two types of live rock you used. Did you see any difference in the type or amount of sponges between Live A and Live B? I ask because Haas, et al,¹ ² ³ has shown DOC released by corals and especially labile DOC released by algae influences the types of bacteria and de Goeij ⁴ has shown cryptic sponges remove labile DOC roughly a thousand times faster than bacterioplankton (30 min. vs 20 days). Could the differences you documented between Live A and Live B possibly be attributed to cryptic sponges?

Thanks for your post and the links, its great getting to discuss these data with people who have been reading and thinking about these topics for a while.

Sponges... I have to say, neither rock was loaded with sponges but if either was, it would be live rock a. Live rock a had honestly the most beautiful surface growth I've ever seen on live rock, bar none. Tunicates, bryozoans, corals, a few sponges. But I emphasize, it was all on the surface.

Because my tanks are small, I had to break some of the rock to fit it in the rock chamber. In the process I couldnt help but notice that live rock a was *fake* live rock. Some kind of concrete material that had been dyed purple. It was entirely non-porous; there were no inner chambers for sponges (or bacteria, for that matter) to hide in. Even though this rock was shipped wet and stored in good conditions, all the surface life died within a week or so of arrival, and little of it was still present during this experiment.

Live rock b in contrast is very very porous, being composed of real coral rubble. I have seen no visible animal life except for a single aiptasia.

With only two batches of rock compared, I just don't have the data to draw conclusions about *why* they differed. I'd really like to see more sources tested. I can only point out that in this case, counter intuitively, the rock with more visible animal live was demonstrably worse. But of course I don't think it was the animal life; I speculate it was more about the porosity.

 

[Timfish]

@ AquaBiomics Well, sounds like time for a bigger more elaborate experiment! Seems like the porosity of Live B would harbor quite a bit of the organisms and microfauna essential for a healthy microbiome. I know some of the cryptic sponges de Goeij has looked at are boring sponges and might not be very apparent on the surface of rubble. One of the fascinating discoveries made by de Goeij was some of the cryptic sponges had mitosis rates of just 8 hours but didn't grow. Constantly sloughing off cellular debris at a very high rate is what let's sponges deal with labile DOC so much faster than bacteria.

@ i_am_mclovin I've been very happy with live rock from GulfLiveRock.com. It's collected fresh and besides sponges there's invariably nice tunicates, Halimeda and other neat stuff. Wherever you buy from be sure to get it air shipped to minimize dieoff.

 

[AquaBiomics]

@ AquaBiomics: Well, sounds like time for a bigger more elaborate experiment! Seems like the porosity of Live B would harbor quite a bit of the organisms and microfauna essential for a healthy microbiome. I know some of the cryptic sponges de Goeij has looked at are boring sponges and might not be very apparent on the surface of rubble. One of the fascinating discoveries made by de Goeij was some of the cryptic sponges had mitosis rates of just 8 hours but didn't grow. Constantly sloughing off cellular debris at a very high rate is what let's sponges deal with labile DOC so much faster than bacteria.

@ I_am_mclovin I've been very happy with live rock from GulfLiveRock.com. It's collected fresh and besides sponges there's invariably nice tunicates, Halimeda and other neat stuff. Wherever you buy from be sure to get it air shipped to minimize dieoff.

A bigger more elaborate experiment? Sounds good to me I'd love to repeat with a wider selection of live rock. My experimental tanks are occupied with other things for a while but it's an interesting enough experiment I'd be willing to reboot them all to survey additional live rock. The logistics are challenging but not impossible.

Now you've got me thinking about sponges, I will have to crack a few branches and see if there are any boring sponges visible in Live Rock B!

 

[i_am_mclovin]

I’ve used TBS before. My concern with aquacultured live rock is due to what was stated above. It’s not as porous as real coral skeleton live rock, and could potentially have something in it that causes the “uglys” like diatoms etc.

 

[AquaBiomics]

I wonder if there are any aquaculture operations starting with coral rubble rather than manmade / mined rock? I'm sure there are logistical challenges but I'd love to buy it if it exists!

 

[VR28man]

I’ve used TBS before. My concern with aquacultured live rock is due to what was stated above. It’s not as porous as real coral skeleton live rock, and could potentially have something in it that causes the “uglys” like diatoms etc.

Yeah, I think the generally use Walt Smith 2.1. A google search suggested that it's fairly good and porous. (in contrast, Real Reef brand rock at least used to be infamous for the kind of non-porousity mentioned in @AquaBiomics experiment.

 

[hart24601]

I do think these tests may be of value as we get more results in, however from this experiment it seems the best we can say is live rock *might* help with the ugly initial stages since it appeared one group of the 2 LR appeared just as ugly or worse than the dry. My take away from this is LR very well might *not* be an improvement when starting a new tank. LR might be better, but since when LR shopping we have no idea the biome of the rock nor what to look for in the biome (yet) even if we had that information, it would seem from the aquarium results it’s a toss up.

 

[Paul B]

I realize many people can't do this (or look as good as me in a bathing suit) but all through the life of my tank I tried to go to a muddy, salt water bay and find porous rock to add to my reef. Those rocks I find are teeming with life as copepods, amphipods, worms, algae, sponges and bacteria.;

I am sure much of the stuff died or was taken over by the other stuff, especially tropical stuff in my tank but it seems to drastically expand the life and microbiome in my tank and provide much needed breeding populations of tiny creatures for food.

The downside is that I also get different types of algae and cyano which I occasionally get cycles of .
Some of it is good and some a nuisance.


These tiny 1/4" rock anemones came in on a rock.

 

[Retro Reefer]

Great article and confirmation of what I have always known about real live rock Vs dry or man made rock.. I currently have one tank that was established with man made rock and one tank established with ocean aquacultured rock, the differences are undeniable.

 

[Belgian Anthias]

About " live rock"

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

To be able to have a discussion about the effect of the addition of so-called " life rock" one has to define " live rock" . What should be on the rock to be called " live rock" to be used in a reef aquarium. Any rock which has been in a certain environment for a certain period of time may be considered to be " live rock".

What diversity are we talking about?

At the beginning of reefkeeping corals were collected together with there base, the rock on which they were growing, later called " live rock". They had very good results, the bio-load was kept very low. What they did not know at that time is maybe they introduced this way most of the coral holobiont. Introducing some rock which has been in the ocean somewhere on the other end of the world does not introduce a coral's holobiont. After decades of promotion there is still no proof so-called " life rock " would be of any benefit for the reef in a closed system, maybe one is only introducing competitors for the corals?! Who will tell?

Maybe this discussion may add something to the mystery?

 

[Filipabp]

These are the kinds of threads that I absolutely love. Great work, and such an interesting read! Just shows there is so much more to learn in this hobby still. I feeling buying a little liverock just to rejuvenate the microbiome in my tank

Perhaps a lot of hobbyists using only dry rocks will introduce new bacteria through the frags that they add in time?

Also, reading this reminds me of when I initially started my first tank. I used a little dry rock, and then some live rock from different regions of the world because I had a feeling that it would increase the diversity.. The tank never had any of the ugly stages, and people in the local community were sure it was because the tank hadn't cycled yet... Lots of newbies are told to go only dry rock, and it seems to result in months of waiting, and long battles with the uglies which I imagine could be very off-putting from the hobby.

 

[AquaBiomics]

I do think these tests may be of value as we get more results in, however from this experiment it seems the best we can say is live rock *might* help with the ugly initial stages since it appeared one group of the 2 LR appeared just as ugly or worse than the dry. My take away from this is LR very well might *not* be an improvement when starting a new tank. LR might be better, but since when LR shopping we have no idea the biome of the rock nor what to look for in the biome (yet) even if we had that information, it would seem from the aquarium results it’s a toss up.

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_am_mclovin]

Yeah, I think the generally use Walt Smith 2.1. A google search suggested that it's fairly good and porous. (in contrast, Real Reef brand rock at least used to be infamous for the kind of non-porousity mentioned in @AquaBiomics experiment.

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!