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

taricha

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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.









And here's Idea 2a and 2b in post 51 - all the biodiversity numbers followed the same trend of a drop and then rise during the 15 weeks, but the balance scores went different directions - likely more reflective of different progression of the tanks.

Idea 3 in post 73 - 50th percentile diversity was really hard to acheive, only 1 tank got there. But most tanks got to 50th percentile balance, and some quickly.

here's a rundown of what aquabiomics has measured or concluded about many Frequently Asked Questions regarding hobby tank microbiomes in post 101

Idea 4 in post 110 - Not every bacteria you add actually becomes part of the community in the system, even major bacterial families sometimes don't transfer over.

Idea 5a in post 129 - every BRS test tank had the same uncommon family as a major part of the system during the 15 weeks. Not totally clear why.

Idea 5b in post 157 - aquabiomics did mutliple tests with adding material to new or established systems that superficially looked similar to BRS tests - but resulted in far far more diverse results in a much shorter time frame. Maybe live rock and sand can be dramatically different in the microbiome they seed.

Idea 6 in post 227 - There were groups of tanks that converged to similar results by the 10 and 15 week tests. This is seen hobby-wide, many tanks converge to similar long-term communities. But not all tanks do - some converge to a different community and some of the BRS tank communities didn't look like any of the others at 10-15 weeks.
Additionally - 5 tanks that looked near-identical in community at week 10, went totally different directions by week 15. Maturation of a bacterial community is likely a very slow process and there were still effects pushing tanks in different directions between weeks 10-15.

My attempt at some sort of conclusions in post 229 - microbial stability takes a long time, can be lost when the tank does through big disruptions and can be restored over time.
 
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Garf

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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.





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?
 

brandon429

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we are putting a lot of trust into the dna sampling and readout portion of the data analysis, Randy doesn't buy into it's unquestioned validity in posts I read that discuss aquabiomics data. that doesnt mean some viewing window of actual clades at work isn't valuable, it's +1 step up from previously no viewable window for reef tank patterning though because its not like a slew of samplers were growing out swabs on selective agar to see what the initial appearance of alternation of generations looks like per bacterial groups

but there's a limit to how much we can see nowadays... I'm not sure aquabiomics data is free from gimmick but I could be wrong. It would help me trust it more if Randy bought into it lock stock and barrel

from the several readouts I've seen on ab dna-sampled tanks, its at least fair to say the clades always change away from initial strains/what was dosed as bottle bac or imported via live rock and then begin grouping into predictable strains given certain time/maturity intervals. at least some sort of viewing window is present, not bad for first gen dna sampling of reef tank biota.

*it would be neat to take their most recommended approach, for the least invasion, and start new tankers on that direction so we can track application a year from now with hundreds of aimed starts.
 

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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.
 
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taricha

taricha

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Dont you think the bacterial diversity of a mature reef is ultimately a result of the foods fed....
I think we'll need to talk about this, and scratch our heads a little bit as to why the Dry Rock, Dry sand, nothing added "control" finished above half the tanks in Biodiversity score after 15 weeks.
:)

Screenshot_20230318_181016_YouTube.jpg
 

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Climax community AKA final stage of biological succession is obviously different in nature ( Coral Reef) than in reef aquarium. In nature there are abundant sources adding new organisms, in aquarium there must be slow shift towards less abundance. By virtue of smaller size it is inevitable that our Aquarium Reef Systems are less stable than nature and I feel we need to add some extra organisms now and then, like swap some live rock for a new one, few, new CUC members etc. Less chemical and physical stability in our tanks also stresses our biome more and some unfavorable shifts can happen. In a stable tank even pests can have their place. One of my aquariums was overgrown by Majano, but they barely thrive in a different tank and seem to be of no harm ( for now). I am a big fan of balanced, biodiverse tank, but it is a process, not a steady state.
 
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taricha

taricha

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Aquabiomics is a joke. Not a lab. At hobby pricing nobody should really expect more
Are you saying that what they measure is of little importance (a widely held opinion)? Or are you saying that they do a bad job of measuring what they do (an uncommon opinion)?
 

Sean Clark

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Are you saying that what they measure is of little importance (a widely held opinion)? Or are you saying that they do a bad job of measuring what they do (an uncommon opinion)?
I am saying that the report provided for what they measure is of little value and also that they openly acknowledge that their process cannot produce a full sample of what is in the system.
I cannot speak as to how good of a job they do measuring what they do measure.
 

Cichlid Dad

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I started my reef tank based on this series. I started my first reef tank July of last year and have documented the tank on my YouTube channel I don't talk but uploaded video from start until now. It really helped me. I didn't have a real bad ugly faze and it was My first salt water tank
 

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Mature reefs have lower diversity, apparently. Why would increasing diversity help? That tank has become mature and apparently successful. Has diversity anything to do with that? There’s a million interactions between bacteria, their exudates etc that effect other organisms. I doubt humans are clever enough to work it out. Now, robots like me, that’s a different situation :)
 

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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.
 

GlassMunky

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Are you saying that what they measure is of little importance (a widely held opinion)? Or are you saying that they do a bad job of measuring what they do (an uncommon opinion)?
Both in opinion
 

FlyinAg

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I watched those series and thought they were pretty well done. However It seems like biodiversity is used to mostly describe bacteria and other microbial life forms, while things like pods, worms and other good 'hitch hikers' don't really get counted. Pods were added to those systems via jars manually, not via live rock along with all the other critters as we would have done 'back in the day.'

In their tests the pods unsurprisingly seemed to have a pretty positive effect on 'balancing' the system by eliminating uglies or undesirable biodiversity. Anyone who uses real live rock probably has anecdotal experience with this. Thus, the good hich hikers should be included in the definition of biodiversity, and not be an afterthought as they are probably one of the drivers which move the system towards 'higher balance' and less overall diversity.

Ultimately, in my opinion, this highlights one of the big flaws in the 'sterile' tank method and also highlights that we have probably brought some of the issues upon ourselves with dry rock and sterile systems. Of course they are low diversity initially and if there is less diversity it would make sense there are less types of organisms present to compete, thus things appear balanced sooner even though the uglies are still present. But, without the other larger organisms is the system really diverse and balanced?
 

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I watched those series and thought they were pretty well done. However It seems like biodiversity is used to mostly describe bacteria and other microbial life forms, while things like pods, worms and other good 'hitch hikers' don't really get counted. Pods were added to those systems via jars manually, not via live rock along with all the other critters as we would have done 'back in the day.'

In their tests the pods unsurprisingly seemed to have a pretty positive effect on 'balancing' the system by eliminating uglies or undesirable biodiversity. Anyone who uses real live rock probably has anecdotal experience with this. Thus, the good hich hikers should be included in the definition of biodiversity, and not be an afterthought as they are probably one of the drivers which move the system towards 'higher balance' and less overall diversity.

Ultimately, in my opinion, this highlights one of the big flaws in the 'sterile' tank method and also highlights that we have probably brought some of the issues upon ourselves with dry rock and sterile systems. Of course they are low diversity initially and if there is less diversity it would make sense there are less types of organisms present to compete, thus things appear balanced sooner even though the uglies are still present. But, without the other larger organisms is the system really diverse and balanced?
I agree that the micro life like worms, pods, sponges, etc., should be included in the count.

Back in the day when Ron Shimek was discussing deep sand bed health, he had a criteria and a simple counting system for the micro life in a sample of sand. Of course he based the sampling criteria of the bed on the numbers of organisms per foot of sand and not the different species in that foot of sand.

I used his method to collect some samples from two beds and was in the healthy range, but I still questioned the validity. What would be more diverse, a population of all amphipods or a population of several pod species, worms and a couple brittle stars?
 

JoJosReef

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I think we'll need to talk about this, and scratch our heads a little bit as to why the Dry Rock, Dry sand, nothing added "control" finished above half the tanks in Biodiversity score after 15 weeks.
:)

Screenshot_20230318_181016_YouTube.jpg
Likely because there are no replicates and thus no measure of variance. Error bars would tell us a lot on this graphic :)
 

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