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

[taricha]

• What is the definition of diversity as it relates to keeping marine aquariums
• Is there a benchmark or reference

just the total detected number of types of bacteria.

Is it additive such that I can buy a tin of A and add it to B and the new test should include both

yes, it would detect the sequences in A and B - with a caveat, it has a lower limit of detection based on how many sequences are in sample.
If I have 100 detected types, then dump in a whole bunch of sugar, a few types will multiply massively, so then if I sample again some of those low detected types will be statistically a smaller portion of the sequences - so they might below the detection limit.

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)

maybe and hard to say, see below.

Q11 How do we know that any particular family, or microbial diversity, or any other measured difference is important for corals?
LinkQ11
We don’t. No experiment demonstrates that, and you can always find some happy tank with an undetectable level of whatever particular bacteria you are interested in. The argument for these things is trying to mimic nature.

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.

see if 1) seed material could dramatically affect the microbiome, and 2) if the microbiome differences were reflected in algae growth differences. 3) could it be done quickly. and 4) could it be done without cuc / herbivores, to lower the reliance on snails/fish etc to constantly keep the tank from being overrun.

 

[areefer01]

just the total detected number of types of bacteria.


yes, it would detect the sequences in A and B - with a caveat, it has a lower limit of detection based on how many sequences are in sample.
If I have 100 detected types, then dump in a whole bunch of sugar, a few types will multiply massively, so then if I sample again some of those low detected types will be statistically a smaller portion of the sequences - so they might below the detection limit.





maybe and hard to say, see below.



see if 1) seed material could dramatically affect the microbiome, and 2) if the microbiome differences were reflected in algae growth differences. 3) could it be done quickly. and 4) could it be done without cuc / herbivores, to lower the reliance on snails/fish etc to constantly keep the tank from being overrun.

Thank you for the reply. I appreciate it. I'm still not sure about the end goal but I'll do some more homework. At the moment I think it is a number and 90% of the hobbyist won't know what to do with or interpret the results leading them to chase yet again another number. Of course I very well could be wrong (probably the case).

I'll say this as an active scuba diver I've never seen a pristine reef without herbivores. I've seen dead reefs without them.

Again thank you. Stay amazing!

 

[sixty_reefer]

M

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.

I believe the interpretation of diversity as aquabiomics testing is not being fully understood, I had the opportunity to read all the organisms that aquabiomics test under diversity in their rubble and there was many types of diatoms, dinoflagellates, algaes etc.. showing up under diversity not just bacteria this may be the reason that some of the worst systems in the test end up with a higher diversity wile the “balance” is a measure of the right type of organisms score taken from diversity.

this means that if I have a system full of different nuisances I could have a fairly diverse tank although diversity in that situation wouldn’t be a positive thing.

 

[Dan_P]

M

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.

Just wondering if we have hard data that most systems (which ones?) converge to a similar bacteria (not sure your statement was limited to bacteria) biome? The idea seems plausible.

 

[taricha]

At the moment I think it is a number and 90% of the hobbyist won't know what to do with or interpret the results leading them to chase yet again another number.

Fair concern, I think the data we've seen so far says that microbial diversity may be only slightly desirable, and is certainly not a chase-worthy thing for a hobbyist.
Right now the hobbyist reaction to a diversity score should be:
High diversity: "cool"
Low diversity: "huh, weird"
...and move on.

I'll say this as an active scuba diver I've never seen a pristine reef without herbivores. I've seen dead reefs without them.

Yep. I love my urchins and foxface. I'd hate to have to tell people that every tank needs urchins and a foxface - that would be ... a lot of foxfaces.

Just wondering if we have hard data that most systems (which ones?) converge to a similar bacteria (not sure your statement was limited to bacteria) biome? The idea seems plausible.

One minor complication on the "convergence" idea. At the very beginning, Aquabiomics found ("How aquarium microbiomes differ") that yes, tanks converge. But not all to the same microbiome. There are different communities that can be converged to.


Chart from linked article is by doing Principle Component Analysis - where you statistically hunt for the fewest number of variables (hopefully 2) that well-describes similarities and differences between your samples. Plot those variables on your x and y axes, and hope you don't need more than two variables.


(a) represented what was dubbed the "consensus" microbiome - because it was similarly acheived by a bunch of different people (different colors) running different tanks in different places.

You and I would love to see what a chart of this sort looks like now that N = hundreds to thousands of tanks, and try to work out what real variables those different converged communities represent.

 

[taricha]

I had the opportunity to read all the organisms that aquabiomics test under diversity in their rubble and there was many types of diatoms, dinoflagellates, algaes etc.. showing up under diversity not just bacteria

Where'd you read that?
(Even if the types of diatoms and algae etc were lumped in and counted as microbiome diversity - the number of algae types would be small compared to the detected bacterial types. )

 

[sixty_reefer]

Where'd you read that?
(Even if the types of diatoms and algae etc were lumped in and counted as microbiome diversity - the number of algae types would be small compared to the detected bacterial types. )

It was on a thread were we were discussing the aquabiomics rubble. In the certificate had all the species that I believe were considered diversity. Maybe @AquaBiomics could clarify if only bacteria is taken into account under diversity.


Post in thread 'Not gonna lie looks like snake oil'
https://www.reef2reef.com/threads/not-gonna-lie-looks-like-snake-oil.939082/post-10635410


Post in thread 'Not gonna lie looks like snake oil'
https://www.reef2reef.com/threads/not-gonna-lie-looks-like-snake-oil.939082/post-10635409

 

[LobsterOfJustice]

c) live sand and mud
LinkQ3c
Added when sand nuisance looks not good - written up as R2R article. Some live rock/sand/mud material tests positive for pathogens, like uronema.

linkQ3c2
Tested two sources of live sand. One was fine, one had a batch with high levels of uronema.

What were the two sources and what were the results? Sorry the linked video is over a hour long.

 

[sixty_reefer]

@taricha

quote from aquabiomics

“The Diversity score is simply the number of different types of Bacteria or Archaea in your sample”

What does Diversity mean?

Microbiome testing for aquariums and aquaculture

aquabiomics.com

from the web

eukaryotes are in the archaea group

this to me means that all Cyanobacteria types, diatoms, dinoflagellates etc will be considered diversity.

 

[Dan_P]

Fair concern, I think the data we've seen so far says that microbial diversity may be only slightly desirable, and is certainly not a chase-worthy thing for a hobbyist.
Right now the hobbyist reaction to a diversity score should be:
High diversity: "cool"
Low diversity: "huh, weird"
...and move on.


Yep. I love my urchins and foxface. I'd hate to have to tell people that every tank needs urchins and a foxface - that would be ... a lot of foxfaces.



One minor complication on the "convergence" idea. At the very beginning, Aquabiomics found ("How aquarium microbiomes differ") that yes, tanks converge. But not all to the same microbiome. There are different communities that can be converged to.


Chart from linked article is by doing Principle Component Analysis - where you statistically hunt for the fewest number of variables (hopefully 2) that well-describes similarities and differences between your samples. Plot those variables on your x and y axes, and hope you don't need more than two variables.


(a) represented what was dubbed the "consensus" microbiome - because it was similarly acheived by a bunch of different people (different colors) running different tanks in different places.

You and I would love to see what a chart of this sort looks like now that N = hundreds to thousands of tanks, and try to work out what real variables those different converged communities represent.

Yes, Aquabiomics needs to report on their principle component analysis, even if it proves to be useless. I think we could try PCA on the BRS data set. I don’t have the software so I am considering othe cluster analyses that I could implement. I would start by looking at the difference from control study I shared with you. Those results seem to hint at clusters already.

 

[areefer01]

Yes, Aquabiomics needs to report on their principle component analysis, even if it proves to be useless. I think we could try PCA on the BRS data set. I don’t have the software so I am considering othe cluster analyses that I could implement. I would start by looking at the difference from control study I shared with you. Those results seem to hint at clusters already.

Touching upon the report for a minute. Are they still doing personalized follow up emails to help the hobbyist interpret results? I remember getting the first email with results to review then a second email to talk about my results with their assessment. Sent in follow up questions, received an email back.

Or has the volume increased such that it makes it impossible to do these days.

 

[Lineatus]

eukaryotes are in the archaea group

this to me means that all Cyanobacteria types, diatoms, dinoflagellates etc will be considered diversity.

no, archaea are prokaryotes. Archaea and eukaryotes are in sister groups, not the same one.

 

[sixty_reefer]

no, archaea are prokaryotes. Archaea and eukaryotes are in sister groups, not the same one.

You’re right, this terminology is a grey area to me, this would mean only Cyanobacteria could be included in this group as a nuisance.

 

[taricha]

What were the two sources and what were the results? Sorry the linked video is over a hour long.

linkQ3c2
Tested two sources of live sand. One was fine, one had a batch with high levels of uronema.
That link should go to the timestamp in the video where he talks about it - if not it's 1:13:36. He doesn't name the sources. Just that there are bags of live rock and sand that you can buy that he detects fish pathogens in (mostly uronema).
If you want to see the article about when he added sand & mud to his systems it's here.
https://www.reef2reef.com/threads/e...ies-in-my-tanks-updated-with-new-data.684209/
If you want a batch of live sand that you know is of high diversity and was tested and found to contain no known pathogens - you're in luck. Aquabiomics sells just such a thing . (but they are frequently sold out because ...well... pathogens show up in a lot of the batches of raw material they get.)

Touching upon the report for a minute. Are they still doing personalized follow up emails to help the hobbyist interpret results? I remember getting the first email with results to review then a second email to talk about my results with their assessment. Sent in follow up questions, received an email back.

Yes. Eli talks about how this data is by nature complex and confusing, and so he always sends his personal interpretations of the report. (Additional replies back are hit and miss, maybe more likely if the questions are simpler.)

this would mean only Cyanobacteria could be included in this group as a nuisance.

There are, technically other photosynthetic bacteria that could show up in this group, the PNS bacteria would - if detected - show up here as well. But only photosynthetic "nuisance" likely to be detected in the bacteria + archaea group is the cyano like you said.

Speaking of the Purple Non-Sulfur bacteria, @Kenneth Wingerter I think in some of the Q&A I saw with Eli Meyer, maybe you were asking questions about how a hobbyist could go about doing some alternate sampling techniques to better capture the anaerobic bacterial community where microbes like the PNSB might be found.
Do you have any more thoughts on that? Did anybody ever mess around with aquabiomics sampling of anaerobic communities?

 

[taricha]

I think we could try PCA on the BRS data set. I don’t have the software so I am considering other cluster analyses that I could implement. I would start by looking at the difference from control study I shared with you. Those results seem to hint at clusters already.

I'd be wary of doing any stats so fancy (PCA) that I was fuzzy on how exactly they connect to the underlying data.
I like your manual analysis better. Made it pretty clear that there was a set of tanks Including the control that converged to a cluster. At some point we should talk about what that means for those materials that converged to a microbiome a lot like the dry sand and rock.
With only 12 tanks - I'm not sure we'd be lucky enough to get any other clear clusters, but I haven't looked thoroughly at it.

 

[Dan_P]

I'd be wary of doing any stats so fancy (PCA) that I was fuzzy on how exactly they connect to the underlying data.
I like your manual analysis better. Made it pretty clear that there was a set of tanks Including the control that converged to a cluster. At some point we should talk about what that means for those materials that converged to a microbiome a lot like the dry sand and rock.
With only 12 tanks - I'm not sure we'd be lucky enough to get any other clear clusters, but I haven't looked thoroughly at it.

I did some 3D correlations today. Nothing earth shaking came of it but an hour of fun. I’ll share the analysis.

 

[Spare time]

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.

I agree that this is being looked into way too much. What I see when I look at their results is that I have learned nothing from the video. Why? Because its not a good experiment by the standards of what is required to be confident in the results. I see it all as events that occurred by chance in unusual environments. The length of this thread is concerning me because again, people in this hobby have little to no experience with properly designing experiments and statistically analyzing results. There is a reason why 99% of research scientists who do this for a living would see these results and say we can't say we have learned anything from them. If they repeated each of the designs over and over and then quantified the results, then we could run stats (can't say which test because we don't have the distribution of the data after repetition) and get some values that would be useful. But one and done runthroughs don't tell us anything. For example, if it rained all day on Tuesday here, and never again for the year, but Tuesday was my only sample, I would think that I live in a rainforest by seeing that 100% of the time it was raining. So each of these results could have been that Tuesday, or maybe two Tuesdays, and so on. These are fun anecdotal observations and we need to stop reading into these as if we have any real results. This whole error is, imo, the main issue when hobbyists attempt to move their hobby thoughts into scientific thought.

 

[Dan_P]

I agree that this is being looked into way too much. What I see when I look at their results is that I have learned nothing from the video. Why? Because its not a good experiment by the standards of what is required to be confident in the results. I see it all as events that occurred by chance in unusual environments. The length of this thread is concerning me because again, people in this hobby have little to no experience with properly designing experiments and statistically analyzing results. There is a reason why 99% of research scientists who do this for a living would see these results and say we can't say we have learned anything from them. If they repeated each of the designs over and over and then quantified the results, then we could run stats and get some values that would be useful. But one and done runthroughs don't tell us anything. For example, if it rained all day on Tuesday here, and never again for the year, but Tuesday was my only sample, I would think that I live in a rainforest by seeing that 100% of the time it was raining. So each of these results could have been that Tuesday, or maybe two Tuesdays, and so on. These are fun anecdotal observations and we need to stop reading into these as if we have any real results. This whole error is, imo, the main issue when hobbyists attempt to move their hobby thoughts into scientific thought.

A fairly concise and solid take down of the BRS study.

 

[areefer01]

A fairly concise and solid take down of the BRS study.

Is that the intent of this thread?

 

[Dan_P]

Is that the intent of this thread?

I don’t think so.

@taricha had the idea to unpack the BRS biome data. I would say that he saw a potentially interesting but untold story. From the length of the post I’d say his story provided interesting reading and stimulated a good discussion.