"Biodiversity is dead, long live biodiversity" 10 month microbiome data from BRStv.

[taricha]

Let's try to illustrate sixty's point here in a chart....

If we evaluate all 12 methods in phase 1, the ones that failed at week 15 were kinda set to fail from day one.
...
I believe all tanks would of done well if rocks, sand, block that have a possibility to contain photosynthetic organisms were added to a dark sump like in tank 6 (dark cured rubble)

The below chart shows my subjective 1-10 "uglies score" at 15 weeks for each tanks, but split them into two groups.
The blue ones (first 7 listed) are ones that had photosynthetic material from lighted system that was placed directly into the test tanks.
The red bars (last 5) are the ones that either had no photosynthetic material, or who had a very extended dark cure time, or were never added to the lighted part of the tank (dark rubble).

I share Ryan's conclusion here that I just wouldn't take lighted material from one system (or the ocean) and put it in a new system in a lighted portion. Not if I wanted to make life as easy as possible, anyway. In the absence of dedicated herbivores from the first week - it's sort of a foregone conclusion, like sixty said.

(I might point out here the similarities between the dark rubble treatment and the aquabiomics article here Establishing a Healthy Microbiome in a New Aquarium Using Live Rock. Interesting to see what results do get replicated.)

 

[metalle]

I believe we are trying to read too much into a hobby experiment on a shoestring budget. The results or conclusions can’t be used to launch a space shuttle, it’s a hobby. Yes, from a scientific standpoint, too many assumptions and gaps. The original intent is good, can new technology help? Is there a way to use technology and reduce problem areas?
Unfortunately with out replicates results can be random occurrence, we won’t know.
However, it offers a good starting point. To pick something out of the air, If I take 10 pieces of similar rock, 10 bags of salt from different documented lots and 3 documented released lots of 3 vendor bacteria or 3 lots of live sand… same operator, 3 samples of surface and 3 samples of water. Lights off. To that point 6-8 weeks (written rationale) What biome distributions would I get? Could I explain why?.
This would only be valid for 1 experiment and those conditions with limited lot variation. If we get similar output, we may be able to say we have input stability and under those conditions predictable output.
In short, long way to go… you can read a little between the lines but tough to conclude.

Don’t get me wrong, love the work done and applaud the effort in looking to find ways to use eDNA from AquaBiomics or any eDNA vendor to make the hobby entry path better.

 

[sixty_reefer]

Let's try to illustrate sixty's point here in a chart....


The below chart shows my subjective 1-10 "uglies score" at 15 weeks for each tanks, but split them into two groups.
The blue ones (first 7 listed) are ones that had photosynthetic material from lighted system that was placed directly into the test tanks.
The red bars (last 5) are the ones that either had no photosynthetic material, or who had a very extended dark cure time, or were never added to the lighted part of the tank (dark rubble).

I share Ryan's conclusion here that I just wouldn't take lighted material from one system (or the ocean) and put it in a new system in a lighted portion. Not if I wanted to make life as easy as possible, anyway. In the absence of dedicated herbivores from the first week - it's sort of a foregone conclusion, like sixty said.

(I might point out here the similarities between the dark rubble treatment and the aquabiomics article here Establishing a Healthy Microbiome in a New Aquarium Using Live Rock. Interesting to see what results do get replicated.)

This graphic becomes interesting if we had the balance for week 15 also, it seems that balance could be reduced by the presence of nuisances, at a quick glance all the higher balance score were given to the systems that didn’t had any apparent nuisance at week 15 with the exception of tank 11 that it seemed that had a persistent case of diatoms, another observation is that in some systems balance reduces as the nuisance started to establish in the system maybe a indication that something is off or a indication of direct competition for nutrients.

1- 72
4- 77
5- 46
7- 51
8- 46
9- 17
12- 1

2- 90
3- 80
6- 81
11- 51
10- 82

 

[sixty_reefer]

I believe we are trying to read too much into a hobby experiment on a shoestring budget. The results or conclusions can’t be used to launch a space shuttle, it’s a hobby. Yes, from a scientific standpoint, too many assumptions and gaps. The original intent is good, can new technology help? Is there a way to use technology and reduce problem areas?
Unfortunately with out replicates results can be random occurrence, we won’t know.
However, it offers a good starting point. To pick something out of the air, If I take 10 pieces of similar rock, 10 bags of salt from different documented lots and 3 documented released lots of 3 vendor bacteria or 3 lots of live sand… same operator, 3 samples of surface and 3 samples of water. Lights off. To that point 6-8 weeks (written rationale) What biome would I get?
This would only be valid for 1 experiment and those conditions with limited lot variation. If we get similar output, we may be able to say we have input stability and under those conditions predictable output.
In short, long way to go… you can read a little between the lines but tough to conclude.

Don’t get me wrong, love the work done and applaud the effort in looking to find ways to use eDNA from AquaBiomics or any eDNA vendor to make the hobby entry path better.

It’s becoming more easier to predict outcomes of intervention in the hobby, discussion like this and others are at the centre of that knowledge. It wouldn’t be to complicated to replicate this tests with similar or better outcomes imo.

 

[Hats_]

I find that statement from Randy confusing, as he states that they decided to avoid biome in a bottle, that was the statement that got me pondering, if they not using bottled bacteria what are they using to complete the nitrogen cycle that once we start looking into it becames obvious that all systems were put through a nitrogen cycle previously to the testing starting.

my interpretation so far is that they are not considering the nitrogen cycle as part of the tanks biome as it’s mainly done with nitrifying bacteria that shows on a separate eDNA sheet.
the biome that they referred during the experiment is mainly heterotrophic bacteria, zooplankton and other organisms that can only be introduced via donor colonies.
The question that raises eyebrows is what product was used to complete the nitrogen cycle as some products can introduce more than just autotrophic bacteria as you know, in a previous post you made a observation that all systems had a family of bacteria in common throughout the experiment (Methylophilaceae), I can’t stop but wonder if some of this species were introduced with the nitrogen cycle and in a way affect the final result.

nitrogen cycle can be completed without bottles, these bacteria generally settle on their own

 

[sixty_reefer]

nitrogen cycle can be completed without bottles, these bacteria generally settle on their own

No question about it although would you add two clownfish from day zero to a brand new system with only two cups of sand from a cycled system? Or would you add two clownfish to a system with just some mud in the Refugium as an only source of bacteria?

the answer is obviously to many of us and therefore it illustrate that all systems were put through a nitrogen cycle beforehand.

 

[Hats_]

No question about it although would you add two clownfish from day zero to a brand new system with only two cups of sand from a cycled system? Or would you add two clownfish to a system with just some mud in the Refugium as an only source of bacteria?

the answer is obviously to many of us and therefore it illustrate that all systems were put through a nitrogen cycle beforehand.

we used to do it with a dead shrimp and just a dead shrimp. will cycle a tank in like a week or 2. Can also be done with ammonia dosing. I think cycling with anything alive in the tank is a bit cruel and with the alternatives that we have it is plainly unnecessary

 

[sixty_reefer]

we used to do it with a dead shrimp and just a dead shrimp. will cycle a tank in like a week or 2. Can also be done with ammonia dosing. I think cycling with anything alive in the tank is a bit cruel and with the alternatives that we have it is plainly unnecessary

I’ve done many nitrogen cycles myself and I know what’s involved in it that’s why I’m sure this systems were put through a nitrogen cycle before hand, BRS would never put the fish through that stress and they said at the beginning that they call this biome cycling that is different from the nitrogen cycle.
the only problem I see is that the nitrogen cycle can affect some of the results by introducing some species of heterotrophic bacteria depending on the method used.

 

[sixty_reefer]

@Hats_ the one that shows clearly that they are pre cycled is tank 5, which consists of dry sand, dry rock and coral as only donor (pretty sure that there is one sps in there also)

can you imagine if anyone on here asks if they could cycle a system with coral and add two fish to it? this illustrates that BRS could technically get away with anything.

 

[Hats_]

@Hats_ the one that shows clearly that they are pre cycled is tank 5, which consists of dry sand, dry rock and coral as only donor.

can you imagine if anyone on here asks if they could cycle a system with coral and add two fish to it? this illustrates that BRS could technically get away with anything.

ahh now i see the meaning of your post haha, i thought u meant that you cant cycle a tank without bottled bacteria lol

 

[sixty_reefer]

ahh now i see the meaning of your post haha, i thought u meant that you cant cycle a tank without bottled bacteria lol

No, just trying to illustrate that this system were cycled before the testing started.

 

[ScottB]

Sorry to be obtuse here… but isn’t that purely expected and logical to begin with?

I think the distinction he is making is one about Diversity Vs Balance. Many of us have long assumed that greater Diversity is the goal, when in fact is Balance works out better.

I have more recently been thinking about it as a "noisy" biome versus a stable biome.

 

[ScottB]

Aquabionetics, also told my reef at the time had less biodiversity than most tanks. And my tank was over 45 years old at the time.

Assuming your tank had a good (reef-like) balance score, your anecdote "fits" the data of the test. Lower diversity, but better balance. Do you recall your Balance score?

 

[beesnreefs]

I think the distinction he is making is one about Diversity Vs Balance. Many of us have long assumed that greater Diversity is the goal, when in fact is Balance works out better.

I have more recently been thinking about it as a "noisy" biome versus a stable biome.

I like this. I think @AquaBiomics might suggest diversity has minimal correlation to healthy reef tanks. Additionally, stability itself may or may not be healthy. The biome could be a stable population of nasty bugs. It’s a stable biome made up of the right kind of critters that seems to correlate to healthy for systems.

For me it’s sort of the difference between having a ton of acquaintances (diversity) v. having a few very close friends (balance). It’s better to have a small number of the “right” kind of supportive people.

 

[BeanAnimal]

I think the distinction he is making is one about Diversity Vs Balance. Many of us have long assumed that greater Diversity is the goal, when in fact is Balance works out better.

I have more recently been thinking about it as a "noisy" biome versus a stable biome.

I think you will find that both logic and data point toward the long term steady state ‘stable’ biomes looking pretty much the same. Our captive systems all somewhat progress toward the same endpoint.

 

[sixty_reefer]

I think the distinction he is making is one about Diversity Vs Balance. Many of us have long assumed that greater Diversity is the goal, when in fact is Balance works out better.

I have more recently been thinking about it as a "noisy" biome versus a stable biome.

I have to say that imo balance has to be the best of aquabiomics testing as diversity doesn’t mean much, Aipatasia and other nuisances could be considered diversity on this type of testing, meaning that low diversity is not always a bad thing to have.

 

[taricha]

Idea 5b: The other big headscratcher (for me) in the BRS results.
Aquabiomics demonstrated in two separate articles (with replicate tanks) that it was possible to add material either to a new system...
Establishing a Healthy Microbiome in a New Aquarium Using Live Rock

...or to supplement an established system...
Effects of live sand & mud on the microbial communities in my tanks
...to quickly (in <4 weeks) increase the diversity of the system to >50 percentile.

But BRS results were that zero out of 12 tanks acheived results like that in 4 weeks - only 1 tank of 12 got to 50th percentile by week 15.

Please excuse this abomination of a chart, but it scales the aquabiomics and BRS data to show the raw number of types of bacteria on the same vertical scale - to illustrate how different the number of families is between the BRS tests and the aquabiomics article tanks.
Left chart is from first aquabiomics article, using live rock in the overflow to seed the microbiome.
Center chart is from the second aquabiomics article where live mud/sand was used to raise the diversity. Right chart is all the BRS data - max # of strains was only over 200 in only one system.

As you can see, All the BRS tanks moved similarly on this scale, and none of the BRS tanks got anywhere near the measured diversity that aquabiomics found repeatedly from adding the material in its tests.

So a couple of different possible interpretations:
Does this mean that the Aquabiomics results were not as replicable as they appeared? Have other people been able to raise their measured microbial diversity dramatically with those materials? (maybe @AquaBiomics could comment)

Or does it mean that none of the 12 starting strategies / materials that BRS did would actually be high diversity material - compared to the aquabiomics article materials?

I don't think it likely that the aquabiomics data / testing noise is the source of the discrepancy - note that the starting diversity of types is pretty similar for starting material in the BRS tests and the aquabiomics articles. Also notice that the BRS most diverse (gulf rock) was not that different from the "live rock A" in the first aquabiomics article.

I think it more likely that the BRS starting media were actually significantly less bacterially diverse than the material that aquabiomics used in their testing.
This is a simpler explanation to me: that the BRS live mud (aquaforest) was not similar to the live mud/sand from floridapets that aquabiomics used, and that the live rock that BRS got was more like the aquabiomics live rock A, than their high diversity live rock B. And transferring some subset of material (rock, sand, dark rubble, water, biobrick) from a medium or low diversity established system to another new system won't lead to high diversity.

If this is correct, then quickly establishing high biodiversity may not be as difficult as BRS data made it look - you just have to keep in mind that not all mud/sand is the same, and not all live rock is the same in that respect either.

 

[areefer01]

Idea 5b: The other big headscratcher (for me) in the BRS results.
Aquabiomics demonstrated in two separate articles (with replicate tanks) that it was possible to add material either to a new system...
Establishing a Healthy Microbiome in a New Aquarium Using Live Rock

...or to supplement an established system...
Effects of live sand & mud on the microbial communities in my tanks
...to quickly (in <4 weeks) increase the diversity of the system to >50 percentile.

But BRS results were that zero out of 12 tanks acheived results like that in 4 weeks - only 1 tank of 12 got to 50th percentile by week 15.

Please excuse this abomination of a chart, but it scales the aquabiomics and BRS data to show the raw number of types of bacteria on the same vertical scale - to illustrate how different the number of families is between the BRS tests and the aquabiomics article tanks.
Left chart is from first aquabiomics article, using live rock in the overflow to seed the microbiome.
Center chart is from the second aquabiomics article where live mud/sand was used to raise the diversity. Right chart is all the BRS data - max # of strains was only over 200 in only one system.

As you can see, All the BRS tanks moved similarly on this scale, and none of the BRS tanks got anywhere near the measured diversity that aquabiomics found repeatedly from adding the material in its tests.

So a couple of different possible interpretations:
Does this mean that the Aquabiomics results were not as replicable as they appeared? Have other people been able to raise their measured microbial diversity dramatically with those materials? (maybe @AquaBiomics could comment)

Or does it mean that none of the 12 starting strategies / materials that BRS did would actually be high diversity material - compared to the aquabiomics article materials?

I don't think it likely that the aquabiomics data / testing noise is the source of the discrepancy - note that the starting diversity of types is pretty similar for starting material in the BRS tests and the aquabiomics articles. Also notice that the BRS most diverse (gulf rock) was not that different from the "live rock A" in the first aquabiomics article.

I think it more likely that the BRS starting media were actually significantly less bacterially diverse than the material that aquabiomics used in their testing.
This is a simpler explanation to me: that the BRS live mud (aquaforest) was not similar to the live mud/sand from floridapets that aquabiomics used, and that the live rock that BRS got was more like the aquabiomics live rock A, than their high diversity live rock B. And transferring some subset of material (rock, sand, dark rubble, water, biobrick) from a medium or low diversity established system to another new system won't lead to high diversity.

If this is correct, then quickly establishing high biodiversity may not be as difficult as BRS data made it look - you just have to keep in mind that not all mud/sand is the same, and not all live rock is the same in that respect either.

Maybe the question(s) should be:

• What is the definition of diversity as it relates to keeping marine aquariums
• Is there a benchmark or reference
• Is it additive such that I can buy a tin of A and add it to B and the new test should include both
• Do we care that our scores are different
• More importantly should we include display photos for correlation of results to display (getting back to basics here in what does a number actually mean)

I'm still not clear what BRS was trying to accomplish with the results (I admit ignorance on my part as I didn't watch the video). If the goal was to circumvent the various phases of a reef cycle or prevent the so called ugly phases why? Reefs take years to develop and herbivores are our friends.

Interesting discussion never the less.

 

[areefer01]

If this is correct, then quickly establishing high biodiversity may not be as difficult as BRS data made it look - you just have to keep in mind that not all mud/sand is the same, and not all live rock is the same in that respect either.

This is why I asked earlier if BRS included a test using live rock, and sand, from TBS. You replied I recall saying they didn't. The could have also included another tank using KP Aquatics. In fact that would have been interesting as their leased waters are in different locations.

But alas time is money so I can understand why they didn't.

 

[BeanAnimal]

M

Maybe the question(s) should be:

• What is the definition of diversity as it relates to keeping marine aquariums

I don‘t think many of you are looking at the data or logical conclusion. In the end, most mature systems end up very similar. A select subset of organisms rise to the top most of the time and the rest are eventually outcompeted or die out.