Should we rethink and refine means and methods for cycling tanks?

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"Why" may be a deeper question than can be answered?
But if you search "coral recruitment" - the process by which a polyp selects where to live and then changes from planktonic to sessile, attaches and grows - that research is all about biofilms, surfaces, coralline algae, and the bacteria associated with the various surfaces. The coral polyps have strong preferences of what they like and don't like - and those preferences have big effects on the survival rates.

just a sampling of two abstracts for flavor...

Thanks. We can always rely on you to find interesting stuff.

OK what about after the larvae settle? In our case, what does a piece of coral flesh care about what biofilm is on the piece of ceramic it is glued to?
 
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It makes a lot of sense that with our low amount of ammonia, that an organism capable of using ammonia to harness the energy of both the ammonia->NO2 and the NO2->NO3 step ought to have some advantages in our hobby systems.
@Lasse I thought about this some more. It doesn't help with the mystery of relatively too few observable nitrite oxidizers compared to ammonia oxidizers in the aquabiomics data set.

in my aquabiomics report, I indeed had nitrospira (the genus in the reference earlier) however it is counted as a nitrite oxidizer - which is traditionally the role of that genus.
So if it were doing both, then it's a "nitrite oxidizer" munching ammonia it's not supposed to.

To account for seeing almost no nitrite oxidizers, we'd have to find a labeled "ammonia oxidizer" that's doing both and munching NO2 secretly. Haven't seen that reported anywhere.
 

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OK what about after the larvae settle? In our case, what does a piece of coral flesh care about what biofilm is on the piece of ceramic it is glued to?
apparently the survival rate even after settling/metamorphosis was correlated to where it settled (end of the the second quoted section).
In that case it was correlated to which coralline algae types each coral made its home on. Not all are equally coral-friendly :)
Another paper I ran across a while back connected which coralline algae types were more and less friendly to corals to the type of DOC released by the coralline algae. More fluorescent DOM (yellow water compounds) from the coralline algae was associated with more growth of bacteria, and was less friendly to corals.
The present study compared the exudates, tissue bound and water column associated microbial communities from two species of CCA belonging to genera that have been previously shown to have different effects on coral larval settlement, H. reinboldii and P. onkodes (facilitating and inhibiting, respectively;

We collected exudates from Hydrolithon reinboldii and Porolithon onkodes in both filter-sterilized seawater and unfiltered seawater from Kāne‘ohe Bay, Hawai‘i. Our results demonstrate that while both species exude equivalent quantities of dissolved organic carbon they differ in the composition of fluorescent DOM and fostered distinct microbial communities. P. onkodes exudates facilitate more microbial OTUs associated with coral disease, whereas H. reinboldii facilitated OTUs known to produce antimicrobial compounds.


If I try to stab blindly at the question "Why would corals care?" the fuzzy picture suggests that corals like to be in control of their own microbiome, and an influx of complicating organic carbon creates bacterial competition that might disturb their preferred community.

If we wildly try to spin this into a story about how to make corals happy in a new tank, then we might guess that corals don't want bacterial competition from established emitters of organic carbon (other photosynthetic organisms).
They might do better if you add them before the uglies, rather than waiting until the uglies have already peaked and subsided. You could say this is probably wrong because it cuts against hobby conventional wisdom derived from years of experience, but some like @Lasse seem to think corals early works quite well.
 
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apparently the survival rate even after settling/metamorphosis was correlated to where it settled (end of the the second quoted section).
In that case it was correlated to which coralline algae types each coral made its home on. Not all are equally coral-friendly :)
Another paper I ran across a while back connected which coralline algae types were more and less friendly to corals to the type of DOC released by the coralline algae. More fluorescent DOM (yellow water compounds) from the coralline algae was associated with more growth of bacteria, and was less friendly to corals.





If I try to stab blindly at the question "Why would corals care?" the fuzzy picture suggests that corals like to be in control of their own microbiome, and an influx of complicating organic carbon creates bacterial competition that might disturb their preferred community.

If we wildly try to spin this into a story about how to make corals happy in a new tank, then we might guess that corals don't want bacterial competition from established emitters of organic carbon (other photosynthetic organisms).
They might do better if you add them before the uglies, rather than waiting until the uglies have already peaked and subsided. You could say this is probably wrong because it cuts against hobby conventional wisdom derived from years of experience, but some like @Lasse seem to think corals early works quite well.
Oh man!
This ones for the straight up heads right here:D
 
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@taricha
Going against conventional wisdom here a little bit and approaching it more from a common sense point of view.
We actually can look at a thriving, healthy system and see that its thriving and made it through all the uglies.
We actually do have a good idea what kind of coraline and bacteria our corals do or dont want growing around them to thrive. Encrusting, coraline, propagating, no uglies etc.
We actually can stock a tank with healthy corals from thriving system and physically observe these interactions happening on surfaces with our own eyes.
We actually can nudge along certain processes by introducing certain things into new tank to help certain interactions happen quicker.
We could also throw a bjd/algae covered coral in separate system and watch that thrive and do the exact opposite.
What am I missing here in the conventional wisdom thats says that stocking a tank responsibly with healthy thriving corals as fast as we responsibly can wouldnt benefit a new tank?
The science kind of shows that its not only plausible to suggest we can but in theory this should maybe be industry standard?
I wonder if @AquaBiomics is looking at these different coralines that corals prefer and exactly what his rubble consists of here.
What in our power could we do differently as far as feeding, system set up and functionality etc to discourage or stop unhealthy coral bacterias to stop growing in our systems besides only introducing what we want in our systems as fast as we responsibly can?

What am I missing here or not wrapping my head around?
 
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@taricha
Going against conventional wisdom here a little bit and approaching it more from a common sense point of view.
We actually can look at a thriving, healthy system and see that its thriving and made it through all the uglies.
We actually do have a good idea what kind of coraline and bacteria our corals do or dont want growing around them to thrive. Encrusting, coraline, propagating, no uglies etc.
We actually can stock a tank with healthy corals from thriving system and physically observe these interactions happening on surfaces with our own eyes.
We actually can nudge along certain processes by introducing certain things into new tank to help certain interactions happen quicker.
We could also throw a bjd/algae covered coral in separate system and watch that thrive and do the exact opposite.
What am I missing here in the conventional wisdom thats says that stocking a tank responsibly with healthy thriving corals as fast as we responsibly can wouldnt benefit a new tank?
The science kind of shows that its not only plausible to suggest we can but in theory this should maybe be industry standard?
I wonder if @AquaBiomics is looking at these different coralines that corals prefer and exactly what his rubble consists of here.
What in our power could we do differently as far as feeding, system set up and functionality etc to discourage or stop unhealthy coral bacterias to stop growing in our systems besides only introducing what we want in our systems as fast as we responsibly can?

What am I missing here or not wrapping my head around?
There is not data to prove that the areas aquabiomics samples from are the 'correct ones' to find nitrifies. The goal (I believe) was to show tank diversity. But As my results show - there are markedly different results - depending on which area of the tank is/are sampled.
 

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There is not data to prove that the areas aquabiomics samples from are the 'correct ones' to find nitrifies. The goal (I believe) was to show tank diversity. But As my results show - there are markedly different results - depending on which area of the tank is/are sampled.
I've posted my experiment - about 5 times - from several areas from my tank which show markedly different results.
 

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@Lasse I thought about this some more. It doesn't help with the mystery of relatively too few observable nitrite oxidizers compared to ammonia oxidizers in the aquabiomics data set.

in my aquabiomics report, I indeed had nitrospira (the genus in the reference earlier) however it is counted as a nitrite oxidizer - which is traditionally the role of that genus.
So if it were doing both, then it's a "nitrite oxidizer" munching ammonia it's not supposed to.

To account for seeing almost no nitrite oxidizers, we'd have to find a labeled "ammonia oxidizer" that's doing both and munching NO2 secretly. Haven't seen that reported anywhere.
Let us put it this way - if there is AOB (or I prefere AOO -> Ammonia Oxidizing Organisms because AOB do not cover the archaeas that is probably the most common AOO in saltwater) - there must be NOB too. If @AquaBiomics not detect them - they are not sequenced species or genus

Sincerely Lasse
 

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apparently the survival rate even after settling/metamorphosis was correlated to where it settled (end of the the second quoted section).
In that case it was correlated to which coralline algae types each coral made its home on. Not all are equally coral-friendly :)
Another paper I ran across a while back connected which coralline algae types were more and less friendly to corals to the type of DOC released by the coralline algae. More fluorescent DOM (yellow water compounds) from the coralline algae was associated with more growth of bacteria, and was less friendly to corals.





If I try to stab blindly at the question "Why would corals care?" the fuzzy picture suggests that corals like to be in control of their own microbiome, and an influx of complicating organic carbon creates bacterial competition that might disturb their preferred community.

If we wildly try to spin this into a story about how to make corals happy in a new tank, then we might guess that corals don't want bacterial competition from established emitters of organic carbon (other photosynthetic organisms).
They might do better if you add them before the uglies, rather than waiting until the uglies have already peaked and subsided. You could say this is probably wrong because it cuts against hobby conventional wisdom derived from years of experience, but some like @Lasse seem to think corals early works quite well.

This is the heart of the discussion - thanks taricha. This is what Im slowly starting to suspect - and what we're hoping we can prove with some dirty experimentation :)
 

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This is the heart of the discussion - thanks taricha. This is what Im slowly starting to suspect - and what we're hoping we can prove with some dirty experimentation :)
I fully agree with @taricha - the more corals added 'soon' - assuming you have a stable system, etc. the better. One issue is that many people starting 'new' tanks do not have the knowledge to maintain that stability. If I were to start a new tank - I would add water rock and corals some bacteria - or an old biofilter of some kind. Follow Alkalinity/Ca until I could figure out dosing requirements - and once stable relatively, add fish.
 
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I wonder if @AquaBiomics is looking at these different coralines that corals prefer and exactly what his rubble consists of here.
No and Yes.
Aquabiomics is trying to provide a "clean" source of reef-associated live rock bacterial diversity to match live rock that he started a few tanks with in this article that gave good results (low amount of uglies, robust nitrification) as compared to another source of live rock that was undesirable in both.
So the concern is not the right kind of coralline necessarily. But also when you buy the rubble you get an exhaustive documentation of the genetic sequences detected in the sample. bacteria and otherwise, so the species of coralline - if it's a known cultured one - gets identified.

in this batch that was posted by a customer there was one type of coralline detected - an unidentified strain.
In my tank, aquabiomics found 3 strains of coralline: "Lithophyllum margaritae" and two uncultured ones.


There is not data to prove that the areas aquabiomics samples from are the 'correct ones' to find nitrifies. The goal (I believe) was to show tank diversity. But As my results show - there are markedly different results - depending on which area of the tank is/are sampled.

Let us put it this way - if there is AOB (or I prefere AOO -> Ammonia Oxidizing Organisms because AOB do not cover the archaeas that is probably the most common AOO in saltwater) - there must be NOB too. If @AquaBiomics not detect them - they are not sequenced species or genus
OR :) alternative hypothesis (to both forms of the sample failure hypothesis) ....
Perhaps in many systems, ~90% of inorganic nitrogen gets consumed by photosynthetic organisms and heterotrophs, so for each 10 parts of ammonia available to ammonia oxidizers, only 1 part Nitrite is available to nitrite oxidizers. in that case we might expect ~ 1/10 the population of NOB to AOO, thus the nitrite oxidizers slide under the aquabiomics limit of detection like half the time.
Even if the swab of the biofilm is the right place to find what you are looking for and the sequences are in the database, it's possible the imbalance is real and not an artifact.
 
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I fully agree with @taricha - the more corals added 'soon' - assuming you have a stable system, etc. the better. One issue is that many people starting 'new' tanks do not have the knowledge to maintain that stability. If I were to start a new tank - I would add water rock and corals some bacteria - or an old biofilter of some kind. Follow Alkalinity/Ca until I could figure out dosing requirements - and once stable relatively, add fish.
Agreed. I think the "chemistry" portion that comes along with reefing can be the most overwhelming part of reefing. The more that clicks that i think i get. The more i learn i really dont know.. Especially when you get into the biology aspect and formulas that mostly only biologists and chemists can really compute and extrapolate from the papers. Let's talk about the papers for a minute. Most need a super good summation put into good old regular people speak for most to understand.
The pros have given us super solid baseline #'s to strive for that im finding as long as I DO keep those #'s within reason that "balance" magically happens. The more diligence i put into keeping those #'s stable and within reason. The faster it actually happens.
I feel like alot of reefers are stuck here.
I have been stuck there. When I read the help threads its mostly people at wits end, putting in all they possibly can, countless hours scrubbing algae, dinos etc. Its not really that they don't have the work ethic or drive for good husbandry its more we could probably could be setting up our tanks much smarter out of the gate so they do much of the hard work for us.
 

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This is the heart of the discussion - thanks taricha. This is what Im slowly starting to suspect - and what we're hoping we can prove with some dirty experimentation

maybe we push the theory to its logical (or absurd) conclusion....
Take dry sterile aragonite sand/rock, use a "pioneer" coral frag (not all coral is equal, if you want acros, dont use a sarcophyton as pioneer). Vigorously swirl the coral frag around in your new salt water dry rock & sand tank. Better if it's an acro that makes more slime.
Place the pioneer frag in the tank, and light it narrowly. Feed the coral a small amount of ammonia drops (no carbon). The system should be initially dominated by the coral microbiome. And the dominant source of organic carbon should be what is produced by the coral itself (slime, etc). This ought to give the system the best chance to become as friendly to the coral as possible.
After a week, you can add some biospira if nitrification is not observed. And maybe a fish and fish food a bit after that.
 

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No and Yes.
Aquabiomics is trying to provide a "clean" source of reef-associated live rock bacterial diversity to match live rock that he started a few tanks with in this article that gave good results (low amount of uglies, robust nitrification) as compared to another source of live rock that was undesirable in both.
So the concern is not the right kind of coralline necessarily. But also when you buy the rubble you get an exhaustive documentation of the genetic sequences detected in the sample. bacteria and otherwise, so the species of coralline - if it's a known cultured one - gets identified.

in this batch that was posted by a customer there was one type of coralline detected - an unidentified strain.
In my tank, aquabiomics found 3 strains of coralline: "Lithophyllum margaritae" and two uncultured ones.





OR :) alternative hypothesis (to both forms of the sample failure hypothesis) ....
Perhaps in many systems, ~90% of inorganic nitrogen gets consumed by photosynthetic organisms and heterotrophs, so for each 10 parts of ammonia available to ammonia oxidizers, only 1 part Nitrite is available to nitrite oxidizers. in that case we might expect ~ 1/10 the population of NOB to AOO, thus the nitrite oxidizers slide under the aquabiomics limit of detection like half the time.
Even if the swab of the biofilm is the right place to find what you are looking for and the sequences are in the database, it's possible the imbalance is real and not an artifact.
I will add a further limitation - what if the area chosen to swab has different biofilm than other areas of the tank (which I think is extremely possible) - differences in flow, light, etc. My GUESS - is that your theory is may be less likely - due to the growth rate of bacteria as compared to other organisms (for example - I believe that nitrifiers have a faster doubling time than algae or zooxanthellae, etc. Additionally looking at some of the stuff Brandon has done (cleaning rocks, etc of algae) - there is no new 'cycle' - thus it seems to me that the bacteria have to be present and more active than other things.
 

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maybe we push the theory to its logical (or absurd) conclusion....
Take dry sterile aragonite sand/rock, use a "pioneer" coral frag (not all coral is equal, if you want acros, dont use a sarcophyton as pioneer). Vigorously swirl the coral frag around in your new salt water dry rock & sand tank. Better if it's an acro that makes more slime.
Place the pioneer frag in the tank, and light it narrowly. Feed the coral a small amount of ammonia drops (no carbon). The system should be initially dominated by the coral microbiome. And the dominant source of organic carbon should be what is produced by the coral itself (slime, etc). This ought to give the system the best chance to become as friendly to the coral as possible.
After a week, you can add some biospira if nitrification is not observed. And maybe a fish and fish food a bit after that.
I guess - BUT - isn't there also a theory out there that you can take dry rock, add nothing, and in xx says - it is also cycled? Without adding ammonia, etc. I would think you'd need to use a large colony. AND - I would also think that the 'coral biome' will grow best on other coral - as compared to all over the tank. My thought was if you added a large amount of coral to the tank up front - the coral would use the ammonia. But - in either case there will eventually be nitrifiers filling their niche in the tank (and other bacteria).
 
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I will add a further limitation - what if the area chosen to swab has different biofilm than other areas of the tank (which I think is extremely possible) - differences in flow, light, etc. My GUESS - is that your theory is may be less likely - due to the growth rate of bacteria as compared to other organisms (for example - I believe that nitrifiers have a faster doubling time than algae or zooxanthellae, etc. Additionally looking at some of the stuff Brandon has done (cleaning rocks, etc of algae) - there is no new 'cycle' - thus it seems to me that the bacteria have to be present and more active than other things.
I see your point here but idk if I'd say that bacteria (bad or not) grow any faster than all other photosynthetic organisms. Especially the good ones our corals actually love. Id go pretty far out on a limb to say that certain coraline, especially the coraline that my corals tend to love and want to drop babies and encrust etc. Ive observed this coraline cover almost entire areas of rock, in a period of about 24-48 hours. That had previously been covered in dinos. I think it does come down to conditions. Proper balance of nutrients like you and other have suggested.
I've also watched certain species of shrooms totally slime out brand new discs pretty much instantly before they decided to sprawl out and begin to walk. As opposed to other species of shrooms wont even open up or think about walking on brand new disc pretty much until that disc starts showing signs that coraline is going to grow.
I think we could look at species specific corals and learn alot. There's tons of variables. I love it
 
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maybe we push the theory to its logical (or absurd) conclusion....
Take dry sterile aragonite sand/rock, use a "pioneer" coral frag (not all coral is equal, if you want acros, dont use a sarcophyton as pioneer). Vigorously swirl the coral frag around in your new salt water dry rock & sand tank. Better if it's an acro that makes more slime.
Place the pioneer frag in the tank, and light it narrowly. Feed the coral a small amount of ammonia drops (no carbon). The system should be initially dominated by the coral microbiome. And the dominant source of organic carbon should be what is produced by the coral itself (slime, etc). This ought to give the system the best chance to become as friendly to the coral as possible.
After a week, you can add some biospira if nitrification is not observed. And maybe a fish and fish food a bit after that.
I love this man. I have observed alot of this with my own eyes among different species of corals. Specifically shrooms but not limited to shrooms.
Green slimer for instance.
I put my slimer in my tank on brand new "unseasoned" frag rack at same time. Both brand new to my tank put in same day.
Slimer slimed heavy. Acted mad but could physically see the slime around base of slimer on rack. As well as back wall of tank adjacent to it. I keep my glass and back wall super clean. May rethink that now and let coraline grow.
Anyhow it slime and covered areas around it before it settled and actually began polyp extension.
Let's talk about brand new unseasoned rack it was set on real quick. The slimer did not start encrusting rack until a cpl different interactions occurred. First a little bit of cyano showed up. Cleaned it off and adjust flow and that straightened out.
After that a little bit of dinos appeared on rack. Immediately took it out scrubbed and rinsed in water change water. Cyano and dinos gone.

This whole entire process took about 7-10 days in my system, on brand new rack, before my slimer started encrusting and growing new limbs.
 

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maybe we push the theory to its logical (or absurd) conclusion....
Take dry sterile aragonite sand/rock, use a "pioneer" coral frag (not all coral is equal, if you want acros, dont use a sarcophyton as pioneer). Vigorously swirl the coral frag around in your new salt water dry rock & sand tank. Better if it's an acro that makes more slime.
Place the pioneer frag in the tank, and light it narrowly. Feed the coral a small amount of ammonia drops (no carbon). The system should be initially dominated by the coral microbiome. And the dominant source of organic carbon should be what is produced by the coral itself (slime, etc). This ought to give the system the best chance to become as friendly to the coral as possible.
After a week, you can add some biospira if nitrification is not observed. And maybe a fish and fish food a bit after that.
Very interesting proposal
 

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Doesn't "new cycle science" say you can add fish like day 1? Bottle bacteria says to add fish immediately. So if we follow "disease protocol" it would be multiple months before a tank gets fish anyway.... so why does it matter? Either way using only or new cycle science and disease prep.... the tank remains fishless for months. This all seems redundant. I think all workable solutions, old and new. Are good to inform people about. It's up to us to be responsible with information and try to make the best decision for our situation. The constant arguing is so nuts lol.
 
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Doesn't "new cycle science" say you can add fish like day 1? Bottle bacteria says to add fish immediately. So if we follow "disease protocol" it would be multiple months before a tank gets fish anyway.... so why does it matter? Either way using only or new cycle science and disease prep.... the tank remains fishless for months. This all seems redundant. I think all workable solutions, old and new. Are good to inform people about. It's up to us to be responsible with information and try to make the best decision for our situation. The constant arguing is so nuts lol.
Stick around its starting to get good:D
No new science. Old science proven time and time again.
Exploration of benefits of stocking tank responsibly as biolaod allows as well as with what we know our corals love and don't love.
Looking at the meat and potatoes of how that occurs on surfaces, understanding that is exciting and an invaluable and priceless tool that can be utilized by all.
 
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