Establishing a Healthy Microbiome in a New Aquarium Using Live Rock

[reefwiser]

How microbes reflect the health of coral reefs

How microbes reflect the health of coral reefs

Microorganisms play important roles in the health and protection of coral reefs, yet exploring these connections can be difficult due to the lack of unspoiled reef systems throughout the global ocean.

www.sciencedaily.com

 

[Matt Carden]

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

Ok so this article is a very hard read for someone like me who doesn't have an educational background in biology, microbiology, etc. Most of it I had to read several times to partially understand. Then I got to these sentences and I thought I was losing my mind: "Another nutritional consideration is that many of the coral bacteria are optional anaerobes. During the day, the coral tissue and boundary layers are highly aerobic due to the production of oxygen by the endosymbiotic algae (Shashar et al., 1993; Kuhl et al., 1995). At night when the tissues, including the mucus, become anaerobic, we suggest that many of the coral bacteria can perform anaerobic metabolism, producing products that can serve as nutrients for bacteria and corals during the day (aerobic conditions). Another nutritional consideration is that many of the coral bacteria are optional anaerobes. During the day, the coral tissue and boundary layers are highly aerobic due to the production of oxygen by the endosymbiotic algae (Shashar et al., 1993; Kuhl et al., 1995). At night when the tissues, including the mucus, become anaerobic, we suggest that many of the coral bacteria can perform anaerobic metabolism, producing products that can serve as nutrients for bacteria and corals during the day (aerobic conditions). Another nutritional consideration is that many of the coral bacteria are optional anaerobes. During the day, the coral tissue and boundary layers are highly aerobic due to the production of oxygen by the endosymbiotic algae (Shashar et al., 1993; Kuhl et al., 1995). At night when the tissues, including the mucus, become anaerobic, we suggest that many of the coral bacteria can perform anaerobic metabolism, producing products that can serve as nutrients for bacteria and corals during the day (aerobic conditions)." So you might want to fix this if you can still edit it. I am reading it in English so it could be a problem with the translator.

Other than that your article was very informative and interesting to know how adaptive coral are.

 

[Belgian Anthias]

So you might want to fix this if you can still edit it. I am reading it in English so it could be a problem with the translator.

Other than that your article was very informative and interesting to know how adaptive coral are.

Thanks to inform me.
I have opened a conversation about the issue.

 

[Chrisv.]

Do you own a miseq?

 

[AquaBiomics]

Do you own a miseq?

I wish! No, I prepare the samples for DNA sequencing (this is the hard part) and send them to a DNA sequencing facility (they have the expensive machine)

But we're working on the funding for our own sequencer which will cut turnaround times in half and expand capacity fourfold. Someday!

 

[Gaspipe]

Excited to get this product into a new tank! @AquaBiomics if you can, please look at my tank build thread. I have some questions. <link>

Thanks in advance!
Gaspare

 

[MnFish1]

Very nice article - it would have been nice to continue the experiment to see what happened over time. Additionally, Seems like there is an issue with live rock A and B (to me - if it was just 'dry rock' vs. 'live rock', Live rock A and B should be much more similar. Lastly - My strong guess is that adding living things to the 'dry rock tank' - would result in a rapidly increasing bacterial population - which in a short amount of time would 'catch up' to the live rock tank.

I am not sure why or where it would be expected that sterilized dry rock would somehow spontaneously generate nitrifiers as quickly as live rock. BUT - no one uses dry rock in this manner. They put rock in a tank, add coral, fish, etc - And the rock itself when put into the tank is not 'sterilized' beforehand.

It woudl have been nice to have another couple controls - 1. Dry rock (not sterilized) 2. Dry rock with some added coral/fish. 3. a longer measurement period - such that you can tell how long it takes for dry rock tanks to match the others. (and when the live rock tank plateaued).

 

[Belgian Anthias]

How compare things which are not comparable?
If it comes to biological filtration capacity we all know the usable space is most important. In an aquarium, rock is grazed constantly. No doubt a layer of some fine sand will beat any so called " live rock" If it comes to bio-filtration. Using sand the capacity is easily adjustable just by adding or removing some sand. If used in a refuge everything is easily manageable.
Nitrification is not only about nitrifiers, it is about bacterial communities working together in a biofilm. Most nitrification takes place in biofilms with a high remineralization capacity, removing the produced toxic ammonia not used up by the film and providing a safely stored nitrogen source for slower growing organisms needed for maintaining the balance between users and producers.
The nitrification grade is linked with the remineralization grade. so, to be comparable one has to know the remineralization grade. If the remineralization grade increases fast, nitrifiers will not be able to follow the growth rate of heterotrophs, also not in an established biofilm on " live rock". If a lot of biowaste is available also the heterotrophic nitrification capacity will increase fast but the moment organic carbon availability decreases, the carrying capacity based on heterotrophs will be lost.
Of coarce a rock covered with " life" will contain all bacteria and archaea needed for to compleet the remineralisation cycle including nitrification and denitrification. Must that rock be a rock which first has traveled around the globe? in the case, why not only import the biodiversity and leave the rock where it is?

 

[brandon429]

Build Thread - My SPS Waterbox Peninsula Mini 15

Beautiful build and scape!

www.reef2reef.com

thats an example of a self cycling system no bottle bac no live rock seed needed, plus outcome updates. Linked here to show the utility possibilities of indirectly inoculated cycles.

 

[brandon429]

see MSteven1 here

Bacteria in a bottle, Myth or Fact

Did the online calc indicate to use one mil in the tank for your gallonage

www.reef2reef.com

that one is even more serious because he didn’t even feed, he merely doubled wait time and then moved significant free ammonia to safe. Perhaps the log scale growth of bacteria occurs after thirty days if totally unfed, didnt see that covered in the article. Full unassisted cycle within sixty days logged.

 

[Timfish]

This seems like a good place to post this paper. It seems a common perception that reefers should strive to maintain a "stable" environment. This research shwoing how variable the microbiome of a system is over a 14 month period even with consistant maintennce and stable environmental and chemical parameters.

https://journals.asm.org/doi/pdf/10.1128/AEM.00179-18

 

[brandon429]

I agree. It boosts the discussion to consider all data pertinent to lab cycling and prep, home cycling and total contamination, supplementation and testing + sampling. It's phenomenal what waiting two months in a home setting can produce.

 

[Nano sapiens]

This seems like a good place to post this paper. It seems a common perception that reefers should strive to maintain a "stable" environment. This research shwoing how variable the microbiome of a system is over a 14 month period shows how even with consistant maintennce and stable environmental and chemical parameters.

https://journals.asm.org/doi/pdf/10.1128/AEM.00179-18

The term 'dynamic equilibrium' comes to mind. When one considers the variability of the microbiome in a stable environment/stable parameters, imagine how much more variability there is when the environment is not stable! No wonder that corals and other invertebrates can be overwhelmed under such conditions.

I consider this paper to be one of the most interesting as it takes a look at not only the microbiomes of different coral reefs (and also corals living in different areas of the same reef), but also the difference in microbiomes during a diel diurnal cycle (def.: any pattern that reoccurs every 24 hours):

https://www.nature.com/articles/s41467-019-09419-z

My comments from a previous post directed at Microbiomics:

"This research deals specifically with the microbial communities on four of the Southern Line Islands (some of the most pristine coral reef communities in the world). Not only the composition of the microbial community is determined (some interesting microbial differences from our reef systems stand out), but it also answers the question of how does the microbial community differ in a 24 hr period? Turns out, the difference is 'day and night', literally! The daytime community makeup is quite different from the one at night. In fact, the difference is more pronounced from day to night in one specific spot than from one island to another island."


This raises the question: 'Does this happen in our captive reef environment, too, and to what extent?'

 

[Timfish]

. . . https://www.nature.com/articles/s41467-019-09419-z . . .

Thanks for the link! I haven't seen that paper.

. . . This raises the question: 'Does this happen in our captive reef environment, too, and to what extent?'

Exactly! How is it moderated by livestock and livestock combinations, equipment, feeding regimes and maintenance methodologies. So much to still to learn. :/

 

[VR28man]

Umm I don't think there is such a thing as a "stable" aquarium or ocean. The real world is not Conway's Game of Life.

In the ocean, you have seasonal changes in tides, seasonal blooms of stuff, and upwellings from the deep, etc. before you even talk about runoff from the nearby land, or pollution. The closest thing to "stable" would be a sea mount way in the middle of nowhere in the pacific near the equator.

Same thing with an aquarium. Even in an aquarium with very few changes - say a consistently and well filtered/skimmed and dosed coral only aquarium with consistent water changes - for (say) two years, you still will have at least small changes in biological output and changes in microbe lifestyle - to say nothing of changes due to coral growth*. Adding fish greatly changes the variables in the system, to say nothing of the accumlution of stuff if you don't skim, if you don't change the water, etc. (AKA Old Tank or Lazy Axe Reefer Syndrome -> and note no one advocates a true no-water-change system; wastes do need to be removed).

So anyway, growth of our corals/fish, waste, inevitable changes in feeding patterns and microscopic processes all will change in a tank.

I think what people are saying is to try to be consistent so you minimize the amount of disruption in the system. That is, change the same amount of water in the same period of time, feed the same amount, etc. so as many processes as possible become and stay relatively stable?


* check out the "smallest acro tank" thread where the OP doses a massive amount of extra stuff every day and still claims his levels are a bit lower than normal, since he's loaded with acros that absorb so much. If he did not dose all that stuff, I bet his acros would not only not look as good, but he would run a high risk of a number of them dying, tank crash, etc.

 

[Nano sapiens]

I think what people are saying is to try to be consistent so you minimize the amount of disruption in the system. That is, change the same amount of water in the same period of time, feed the same amount, etc. so as many processes as possible become and stay relatively stable?

Yes, this is spot on! As reef keepers we can only attempt to provide the system as much stability as we possibly can. IMO, there is really nothing to be gained by worrying too much about that which we can't control.

* check out the "smallest acro tank" thread where the OP doses a massive amount of extra stuff every day and still claims his levels are a bit lower than normal, since he's loaded with acros that absorb so much. If he did not dose all that stuff, I bet his acros would not only not look as good, but he would run a high risk of a number of them dying, tank crash, etc.

Yes, I stumbled upon this last week (5g, I believe?). Man, that's a handful to keep going well!

On the flip side, a small mixed reef with stony corals (can include SPS such as Acros) is also doable with a very basic amount of equipment, alk/cal/mag dosing, water changes and a fair amount of reefing knowledge/experience.

 

[brandon429]

Algae/Cyano Issue Not Improving, Help Please?

Hi all, I have a Red Sea Reefer 250 that has been up and running for 8 months now. My issue is a strange black algae\cyano growth that has plagued me for the last two months+. I have been treating as follows: cleaning gravel twice weekly 20% water changes twice a week Addition of beneficial...

www.reef2reef.com

Team don’t think I’m being contrary for any reason other than science is served well in considering opposites


I can’t think of anything shy of sustained antibiotics dosing that should interrupt a microbiome more than that set of moves.


if someone isn’t consistent and is disruptive like that, when will the consequences hit? The bacteria left adhered to rocks even in the face of flushing multiple 100% water changes is diverse enough to carry on ad infinitum it seems. It seems adding things and dosers to the tank causes issues whereas rip cleaning / mass ejection might allow residents to reestablish with less competition? We did reduce waste substrate after all…every single fleck in one pass is ejected. There can’t be a more thorough reef harshing than that, look how happy the updates are

by linking here we can now track updates for the next two years. I bet that reef is never invaded again anytime we check either.

 

[Jgoal55]

What a cool thread! Thanks to all the contributors.

I started my tank (240g total volume) with dry rock mostly because I wanted a very specific aquascape which required assembly and I couldn't do that with live rock because it took so long to complete.

I also used Caribsea “live sand.” I also added pods and microbacter7. Then waited for my cycle to complete and added snails and hermit crabs. I did not add any fish to the aquarium for over 6mos.

in hindsight, I wish I would have added some high quality live rock into the tank to “seed” the dry rock, but I never did.

that said, almost a year after adding the first bit of life, while I still have only 2 entry level corals in my tank (doing very well so far), I have added several fish (about 10 total - 5 of which are medium to X-Large tangs). My ugly stage was very short-lived and now I mostly have the green hard algae all over the dry rock with spots of coraline starting to show up everywhere.

what would be the best way to diversify the micro biome today? Should I just sneak in a few pieces of live rock? (I would first have it in QT at 80.6+ for at least 45days)

 

[MnFish1]

What a cool thread! Thanks to all the contributors.

I started my tank (240g total volume) with dry rock mostly because I wanted a very specific aquascape which required assembly and I couldn't do that with live rock because it took so long to complete.

I also used Caribsea “live sand.” I also added pods and microbacter7. Then waited for my cycle to complete and added snails and hermit crabs. I did not add any fish to the aquarium for over 6mos.

in hindsight, I wish I would have added some high quality live rock into the tank to “seed” the dry rock, but I never did.

that said, almost a year after adding the first bit of life, while I still have only 2 entry level corals in my tank (doing very well so far), I have added several fish (about 10 total - 5 of which are medium to X-Large tangs). My ugly stage was very short-lived and now I mostly have the green hard algae all over the dry rock with spots of coraline starting to show up everywhere.

what would be the best way to diversify the micro biome today? Should I just sneak in a few pieces of live rock? (I would first have it in QT at 80.6+ for at least 45days)

I do not think adding live rock will alter your biome necessarily - instead whatever is in your 'current biome' will likely take over the small pieces of live rock. My comment - if you're not having problems with what you're doing - you don't need to upset the apple cart.

Second - one of the benefits of using 'live rock' - depending which your definition of 'live rock' - is all of the stuff that comes with it. A lot of the 'diversity' you're desiring - is lost during this fallow period at 80.6.

 

[Belgian Anthias]

The best "a live rock" available is a piece of healthy coral . it contains all diversity needed to support the coral and coral holobiont. (ref: MB Anthias 2019)
If a coral is introduced in a new setup, where it would have the best change to survive and grow? Planted on a piece of "life rock" overgrown with periphyton or on a piece of cleaned and sterilized rock introduced together with the coral?