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

[fish farmer]

Likely because there are no replicates and thus no measure of variance. Error bars would tell us a lot on this graphic

Did they sterilize their hands between tanks while setting them up?

 

[JoJosReef]

Study would have been more informative if they ran a third of the conditions and did triplicates.

 

[beesnreefs]

Study would have been more informative if they ran a third of the conditions and did triplicates.

Would you say this “study” provides insufficient data to inform husbandry practice entirely? Or would you say it provides insufficient data to meet publication/peer review standards? Or something else?

 

[JoJosReef]

Would you say this “study” provides insufficient data to inform husbandry practice entirely? Or would you say it provides insufficient data to meet publication/peer review standards? Or something else?

No, it could never be published in a respected scientific journal. If I received this as a manuscript, I'd send it back to the editors with an unfavorable review. Not out of malice, it just lacks experimental rigor.

It is an interesting finding, but as someone previously mentioned, still anecdotal, albeit a good anecdote. Inform husbandry? I think not. I imagine those that are most concerned about pests or prefer the convenience and customizability of a dry system will stick with dry rock/dry sand. Those that believe in biodiversity (like me) will go live rock/sand. Those new to the hobby will likely be confused by this.

 

[cpschult]

Study would have been more informative if they ran a third of the conditions and did triplicates.

Starting here made sense.

No, it could never be published in a respected scientific journal. If I received this as a manuscript, I'd send it back to the editors with an unfavorable review. Not out of malice, it just lacks experimental rigor.

It is an interesting finding, but as someone previously mentioned, still anecdotal, albeit a good anecdote. Inform husbandry? I think not. I imagine those that are most concerned about pests or prefer the convenience and customizability of a dry system will stick with dry rock/dry sand. Those that believe in biodiversity (like me) will go live rock/sand. Those new to the hobby will likely be confused by this.

I think I disagree about those new to the hobby. How many posts daily are made about “what is this, why is my tank ugly” after being up for a few weeks. Helping people make decisions about minimizing the ugly phases of their tanks and helping retain people in the hobby is a win for me.

Do they list genus/species/distribution anywhere or is it just reported as “diversity”?

 

[Randy Holmes-Farley]

I've meant to start this discussion thread for a while... so here we go.

Reef hobbyists have a lot of ideas about biodiversity and what it means in a reef system. A lot of these ideas (mine included) are reasoning from personal experience of myself and others, and how we think it ought to work. Mostly this is because the concepts are fuzzy and we just don't have much data - so reasoning from collective experience is the best we've got in these data-sparse areas.
But that's changing - there are a lot of concepts in this discussion that we now actually have pretty good data to ground ourselves in and think more concretely about - surrounding the concepts of biodiversity, maturity, balance etc. BRS did a series of 11 videos (full playlist) in 2022 "Biome Cycling" involving 12 side by side aquaria run in parallel for 10 months, with detailed observations and data. This was done at a scale and expense that the hobbyist can't duplicate and I think the results are of good quality, and the data is worth digesting even if I don't buy all his reasoning and conclusions. Given how much we think and talk about these ideas like the "ugly phase", biodiversity, maturity, balance etc - this data deserves way more discussion than it has received so far. It's a ton of data, observations, and reasoning to sift through. Way more than one post,
So I'll try to occasionally pull one big idea at a time that I think is well demonstrated by the data, and is worth talking about.

Short summary of the overall exercise. (meet the tanks - Ep 3)
They started 12 tanks from different initial ingredients:
1) Dry sand and Rock - control
2) Dry sand and Rock + Coral frags/colonies
3) Dry rock, live sand in a bag
4) Synthetic live rock cured in seawater
5) Dry Rock and sand + live rock rubble cured in the dark, in dark sump
6) Live Rock and Sand directly from established tank
7) Dry rockand sand + 2 cups of established tank sand
8) Paper-wet indonesian live rock and dry sand
9) Gulf live rock shipped in water and dry sand
10) Dry rock and sand + Aquaforest reef mud
11) Dry rock and sand + 100% water from established system
12) Dry rock and sand + biobrick from established system

All tanks were given two clownfish and were kept dark for 4 weeks, then moderate "LPS lighting" from weeks 5-10, then high "SPS lighting" from weeks 11-15.
They tested each tank via aquabiomics at week 2, week 4, 10, and 15.
(What aquabiomics is and what was measured - Ep 4)


Idea 1: Biodiversity is dead, Balance is the new "biodiversity"
Aquabiomics gives two overall statistical measures/scores:
Biodiversity is a statistical measure of the bacterial families that make up more than 1% of the measured genetic material.
Balance is a measure of how much the present bacterial families look similar to those in established reef systems.

Here's the backwards thing that kills many ideas about biodiversity (like mine). In essentially every system that was started with any live material, The Biodiversity fell while the Balance rose. The biodiversity is initially higher especially in tanks started with a lot of live material like the live rock, but gradually falls. The Balance score - on the other hand, starts extremely low, but in every decent-looking tank climbs over time to more closely resemble typical reef tanks.
So early on, the high biodiversity likely represents a disturbed system, with many food sources of dead, disturbed and out of place organisms, and quick bacterial growth in response - but those early bacterial families look nothing like the eventual expected families that will make up a well-established tank.
Put another way, it is the death and loss of early bacterial diversity that helps shape the microbiome to look more like eventual reef systems. The Balance is a far better measure of this process of moving towards an established system than the biodiversity is, and perhaps the balance score isn't a terrible marker for biofilm maturity and system stability overall.
Ryan explains this idea of high biodiversity in tanks that look awful, and the balance being a better indicator here Ep 7 3:01-3:48

This data is in the videos Ep 5, 6, 7.

Thanks for the nice write up!

IMO, it is interesting and not particularly surprising that tanks tend toward the same microbes over time. Our tanks are good environments for some and less suitable for others.

IMO, it’s an unknown whether it is best to fight against, or at least try to guide this process by adding bacteria, or to go with the flow and let nature pick and choose what is best. I suspect the former may be a losing proposition long term, unless there are specific serious issues at play, such as dinos.

 

[Shibaken3]

I just appreciate that they did such an expensive experiment that I wouldn't be able to do.

 

[JoJosReef]

Starting here made sense.

I think I disagree about those new to the hobby. How many posts daily are made about “what is this, why is my tank ugly” after being up for a few weeks. Helping people make decisions about minimizing the ugly phases of their tanks and helping retain people in the hobby is a win for me.

Do they list genus/species/distribution anywhere or is it just reported as “diversity”?

I think what is confusing about this is the bar graph showing dry rock/sand smack in the middle of the pack. Perhaps the microbiome isn't actually that different over a long period of time, but we have to remember that the guys doing this experiment are experienced reefers, and a new hobbyist might handle arrising situations very differently. Do you think so?

This isn't bad info by any stretch. It's an interesting experiment. Would be great to see a hypothesis tested that >diversity at the start results in fewer episodes of nuisance algae (GHA, cyano, dinos), all other things equal.

 

[Thales]

Dont you think the bacterial diversity of a mature reef is ultimately a result of the foods fed, assuming a little diversity is added each and every time a fish or coral is added?

I have never thought of it that way. I think it is a slug fest between bacteria competing for real estate and in an unstable system, that real estate changes. You can add all the bacteria you want over time, but if the enviornment isn't conducive to that bacteria, or the 'apartment building' is full, that bacteria is not going to thrive or become dominant. Tanks with no or little competition, like dry rock starts, might be able to achieve better balance scores for bacteria sooner because there is less to fight for, they can just kinda move in.

I don't think that getting that balance to be better sooner in the BRS tests means that sterile set ups is superior methodology, but that is my thinking about diversity and balance.

I am not sure we actually care about diversity, we may care more about dominant strains.

 

[Thales]

I've meant to start this discussion thread for a while... so here we go.

Reef hobbyists have a lot of ideas about biodiversity and what it means in a reef system. A lot of these ideas (mine included) are reasoning from personal experience of myself and others, and how we think it ought to work. Mostly this is because the concepts are fuzzy and we just don't have much data - so reasoning from collective experience is the best we've got in these data-sparse areas.
But that's changing - there are a lot of concepts in this discussion that we now actually have pretty good data to ground ourselves in and think more concretely about - surrounding the concepts of biodiversity, maturity, balance etc. BRS did a series of 11 videos (full playlist) in 2022 "Biome Cycling" involving 12 side by side aquaria run in parallel for 10 months, with detailed observations and data. This was done at a scale and expense that the hobbyist can't duplicate and I think the results are of good quality, and the data is worth digesting even if I don't buy all his reasoning and conclusions. Given how much we think and talk about these ideas like the "ugly phase", biodiversity, maturity, balance etc - this data deserves way more discussion than it has received so far. It's a ton of data, observations, and reasoning to sift through. Way more than one post,
So I'll try to occasionally pull one big idea at a time that I think is well demonstrated by the data, and is worth talking about.

Short summary of the overall exercise. (meet the tanks - Ep 3)
They started 12 tanks from different initial ingredients:
1) Dry sand and Rock - control
2) Dry sand and Rock + Coral frags/colonies
3) Dry rock, live sand in a bag
4) Synthetic live rock cured in seawater
5) Dry Rock and sand + live rock rubble cured in the dark, in dark sump
6) Live Rock and Sand directly from established tank
7) Dry rockand sand + 2 cups of established tank sand
8) Paper-wet indonesian live rock and dry sand
9) Gulf live rock shipped in water and dry sand
10) Dry rock and sand + Aquaforest reef mud
11) Dry rock and sand + 100% water from established system
12) Dry rock and sand + biobrick from established system

All tanks were given two clownfish and were kept dark for 4 weeks, then moderate "LPS lighting" from weeks 5-10, then high "SPS lighting" from weeks 11-15.
They tested each tank via aquabiomics at week 2, week 4, 10, and 15.
(What aquabiomics is and what was measured - Ep 4)


Idea 1: Biodiversity is dead, Balance is the new "biodiversity"
Aquabiomics gives two overall statistical measures/scores:
Biodiversity is a statistical measure of the bacterial families that make up more than 1% of the measured genetic material.
Balance is a measure of how much the present bacterial families look similar to those in established reef systems.

Here's the backwards thing that kills many ideas about biodiversity (like mine). In essentially every system that was started with any live material, The Biodiversity fell while the Balance rose. The biodiversity is initially higher especially in tanks started with a lot of live material like the live rock, but gradually falls. The Balance score - on the other hand, starts extremely low, but in every decent-looking tank climbs over time to more closely resemble typical reef tanks.
So early on, the high biodiversity likely represents a disturbed system, with many food sources of dead, disturbed and out of place organisms, and quick bacterial growth in response - but those early bacterial families look nothing like the eventual expected families that will make up a well-established tank.
Put another way, it is the death and loss of early bacterial diversity that helps shape the microbiome to look more like eventual reef systems. The Balance is a far better measure of this process of moving towards an established system than the biodiversity is, and perhaps the balance score isn't a terrible marker for biofilm maturity and system stability overall.
Ryan explains this idea of high biodiversity in tanks that look awful, and the balance being a better indicator here Ep 7 3:01-3:48

This data is in the videos Ep 5, 6, 7.

I love your brain

 

[diveinheadfirst]

It’s crazy how many people bash BRS. They’re attempting to further the hobby by helping people get started in it with as little failure as possible. No, they aren’t phd scientists. To say this wouldn’t make it into a scientific journal is overstating the obvious, and it was never intended to be peer reviewed by the scientific community. I’m grateful for what Randy and Ryan accomplished together and what BRS is still providing. It has helped me a lot. Maybe it’s not for the seasoned vets and that’s okay, but they have a place and serve a much needed purpose in the hobby.

 

[BeanAnimal]

Here's the backwards thing that kills many ideas about biodiversity (like mine). In essentially every system that was started with any live material, The Biodiversity fell while the Balance rose. The biodiversity is initially higher especially in tanks started with a lot of live material like the live rock, but gradually falls. The Balance score - on the other hand, starts extremely low, but in every decent-looking tank climbs over time to more closely resemble typical reef

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

 

[rtparty]

It’s crazy how many people bash BRS. They’re attempting to further the hobby by helping people get started in it with as little failure as possible. No, they aren’t phd scientists. To say this wouldn’t make it into a scientific journal is overstating the obvious, and it was never intended to be peer reviewed by the scientific community. I’m grateful for what Randy and Ryan accomplished together and what BRS is still providing. It has helped me a lot. Maybe it’s not for the seasoned vets and that’s okay, but they have a place and serve a much needed purpose in the hobby.

This.

A lot of people completely miss the big picture with BRS and their testing. They are NOT meant to pass the most rigorous of tests and be peer reviewed. (Peer review is a mostly a joke anyway but that is for another thread.)

The goal in mind with all the BRS videos is to GET and KEEP people in the hobby for as long as possible. This serves two main purposes: it helps people and it helps the business. They really do work together and are much better together than they are alone.

The great thing about this biome test is we can all easily test the theory and see how it works for us. Get a little 10g tank, some dry rock and sand, throw some food and bacteria in, and wait. When the uglies start up, add some pods. Not even $200 tops and that’s buying all new. The pods will be the highest part of the cost. Simple and easy to replicate.

But it seems a good share of people would rather discredit and bash others instead of doing the experiment themselves and fixing the wrongs they saw. That is life these days though.

 

[Court_Appointed_Hypeman]

It’s crazy how many people bash BRS. They’re attempting to further the hobby by helping people get started in it with as little failure as possible. No, they aren’t phd scientists. To say this wouldn’t make it into a scientific journal is overstating the obvious, and it was never intended to be peer reviewed by the scientific community. I’m grateful for what Randy and Ryan accomplished together and what BRS is still providing. It has helped me a lot. Maybe it’s not for the seasoned vets and that’s okay, but they have a place and serve a much needed purpose in the hobby.

It is cynicism. This was a great experiment.

Obviously its too small of a sample and needs to be reproduced a huge amount if times to find trends, but this is a great start.

I understand the issues people might have eith the idea of the control, but I think it makes the most sence, with the fact that it is attenpting to demonstrate what a total lack of deliberate introduction initially means for how the biome will progress. It shows us that addition of microbial life is inevitable, and I also think it demonstrates that diversity doesn't mean balance, as it surpassed diversity of tanks with deliberate addition.

The dry rock doesn't have nearly as much microscopic life going in as the rest, which both means that the organisms that are unser 1% in those other systems may be much more prominent here, because it says nothing of the concentration of these organisms. It also probably means that the battleground is much more protracted with much more empty surface to colonize giving an advantage to hang on or more opportunities to establish where they otherwise may not.

Also, while Randy may only be a customer advocate now, and hold clear biases, i think he does a great job of staying subjective. However no where near to the degree of a completely independent study, he does have bosses now that will probably not like him to be vwry subjective in all cases. I have the feeling while Randy is there to make a hedgefund that bought his company money, he probably has enough say to help push the hobby forward and not just push profitable snake oil.


Lastly, I don't think this did too much product pushing aside from it made me absolutely purchase from algae barn before realizing the hedgefund also owns algae barn. This advertising that the microbiome series served to be, may have also been the trason they got to put the time and money into the endeavor.

We live under capitalism, and everything has to be proffit driven to make it in business, while also the coercion an employer has over an employee, be it implicit or explicit, will absolutely influence any information presented to us from anyone when money is involved. Its important to always be critical of thebinformation we consume, but what BRSTV did here, was pretty dang good all things considered. What BRSTV does in general, is a plus to the hobby regardless of the fact that it probably was a huge increase to the bottom line of the sharks who own so much of this hobby now.

 

[rtparty]

It is cynicism. This was a great experiment.

Obviously its too small of a sample and needs to be reproduced a huge amount if times to find trends, but this is a great start.

I understand the issues people might have eith the idea of the control, but I think it makes the most sence, with the fact that it is attenpting to demonstrate what a total lack of deliberate introduction initially means for how the biome will progress. It shows us that addition of microbial life is inevitable, and I also think it demonstrates that diversity doesn't mean balance, as it surpassed diversity of tanks with deliberate addition.

The dry rock doesn't have nearly as much microscopic life going in as the rest, which both means that the organisms that are unser 1% in those other systems may be much more prominent here, because it says nothing of the concentration of these organisms. It also probably means that the battleground is much more protracted with much more empty surface to colonize giving an advantage to hang on or more opportunities to establish where they otherwise may not.

Also, while Randy may only be a customer advocate now, and hold clear biases, i think he does a great job of staying subjective. However no where near to the degree of a completely independent study, he does have bosses now that will probably not like him to be vwry subjective in all cases. I have the feeling while Randy is there to make a hedgefund that bought his company money, he probably has enough say to help push the hobby forward and not just push profitable snake oil.


Lastly, I don't think this did too much product pushing aside from it made me absolutely purchase from algae barn before realizing the hedgefund also owns algae barn. This advertising that the microbiome series served to be, may have also been the trason they got to put the time and money into the endeavor.

We live under capitalism, and everything has to be proffit driven to make it in business, while also the coercion an employer has over an employee, be it implicit or explicit, will absolutely influence any information presented to us from anyone when money is involved. Its important to always be critical of thebinformation we consume, but what BRSTV did here, was pretty dang good all things considered. What BRSTV does in general, is a plus to the hobby regardless of the fact that it probably was a huge increase to the bottom line of the sharks who own so much of this hobby now.

Aperture/Bertram doesn’t own Algae Barn

 

[Court_Appointed_Hypeman]

Aperture/Bertram doesn’t own Algae Barn

I swote they did, they dont? Well then. That changes a lot

I see I have gotten that from some other posts on here, and took it as fact.

That gives me even higher regard for the micro biome series.

 

[((FORDTECH))]

I’ll just say in my experience when I used Aquabiomics for 6 months the results were iffy at best.
first con is that it takes over a month to get a test sent in, analyzed and get the results. More often than not I was sending in the next months sample before I got my results.

secondly, I once sent the same sample twice labeled differently and it got different results.
I just don’t think these tests are accurate with reproducible results enough to make it any use for a hobbyist.

I wanted to do the same thing with I CP test to prove the same thing but just haven’t had a chance to do it yet but I would guarantee to samples from the same things are going to test completely different at any ICP facility

 

[rtparty]

I swote they did, they dont? Well then. That changes a lot

I see I have gotten that from some other posts on here, and took it as fact.

That gives me even higher regard for the micro biome series.

BRS sells Algae Barn stuff but they don’t own them

 

[rtparty]

I wanted to do the same thing with I CP test to prove the same thing but just haven’t had a chance to do it yet but I would guarantee to samples from the same things are going to test completely different at any ICP facility

Numbers aren’t going to line up perfectly but one isn’t going to read 450ppm calcium and the other reads 325ppm calcium. Well, I can think of one of the ICP companies where this may happen but the better companies will almost always be close enough for our use


Over 40 ICP tests with ATI and I test the big three at the same time of collection. I can’t think of one test where ATI results were totally off base from mine.

The trick is avoiding the crappy companies

 

[danielankeny]

I really believe that people need to understand that what BRS did was simply an anecdotal observation. There is currently no reason to believe that what they showed is not due to chance. This is an issue I have been having with BRS since they want to be more sciencey. They don't have a background in scientific studies or experiments, and so they don't know what their data actually tells them. Nor do they have any background rational to formulate a hypothesis in the first place (albeit Ryan does try to talk to some marine biologists but he doesn't say who and that is very important). There is a reason why every single scientist who goes into the fields of ecology, evolution, and behavior have to also become relative experts in statistical analysis. Even if they did a proper study, no one is replicating or reviewing them, and thus someone else may get completely different results (especially since their studies are correlational not causal, despite them drawring causal conclusions). Also, there needs to be a strong emphasis that, in conclusions, it is better to state that something rejects or fails to reject the null hypothesis rather that creating overly confident statements.

Definitely correct. Need much larger sample sizes to draw definite conclusions