This is what I've dreamed of for so long! Testing for microbes in our tanks!

Randy Holmes-Farley

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I see your results as entirely positive here.

I’m curious what you have seen that you would tag as a negative, aside perhaps from a known human pathogen.
 

AquaBiomics

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I’m curious what you have seen that you would tag as a negative, aside perhaps from a known human pathogen.
I guess I see two categories here - results that are clearly negative (pathogens of fish or corals), and results that deviate from the typical profile. The latter deserve a separate category because there is little evidence (or in many cases, none) that these deviations are harmful, but many of us would still be interested to learn about these deviations.

Clearly negative
I've detected a known fish pathogen and a known coral pathogen each in multiple tanks (1/8 and 1/10 tanks respectively, last time I counted). There are dozens of other known pathogens in the database that are known to occur in aquariums, that I screen for but have not detected yet.

Deviations from typical levels
In terms of deviations from typical levels, its hard to ignore the variation in nitrifying microbes. I think its a complicated subject for a lot of reasons, and I do not consider low (or even undetectable) nitrifying microbes to be necessarily a problem, on their own. Most tanks have measurable ammonia-oxidizing microbes, although at a wide range of levels. A surprising number of tanks lack measurable levels of nitrite oxidizing microbes.

If the system has another mode of dealing with ammonia (e.g. macroalgae), and has no problems maintaining nutrients at the desired levels, this is probably not a problem. There are successful tanks running like that, and why change what's working? But if a tank has no other major competition for nitrogenous wastes, and is struggling with either nutrient levels or algal growth resulting from those levels, low levels of nitrifying microbes suggest a deficiency that can be addressed.

Diversity... if I remember correctly you are not convinced that low diversity is a problem that needs to be addressed, and I agree that most or maybe all of the major questions in this area have not been answered yet. But I'll point out that the starting diversity of a tank is very low, and it remains low for a long time unless we do something to change that. Many of the practices that reef keepers have found to be effective ways of adjusting the ecosystems in their aquariums (including live rock, carbon dosing, and a wide variety of bottled products with undisclosed ingredients) work by manipulating the microbial community, including its diversity. It seems clear that the microbial community is important to the health of our tanks, and diversity is one statistic describing that community.

I'd rather my tank had a diversity more like a thriving reef tank, and less like a brand tank filled with shiny white rocks. I'd consider very low diversity a negative, while acknowledging there are a range of opinions on this (like Mg or alkalinity)

If the composition of the microbial community is very different from the typical tank, I consider that a negative unless the tank has no problems. Balance scores are not intended as a value judgement (bad or good), they're a statistic describing similarity or difference with the typical community.

About half the tanks I sample fall into a cluster of similar communities. Across different users and locations. Meanwhile, other tanks (in some cases other tanks run by the same person) differ from this consensus. Some of those tanks are doing great (although if you talk to their owners, you often find out that they do something very different in their tanks than the average reef keeper). Many are not.

If the tank has a problem without any known cause, and testing reveals that it has a weird microbial community, I consider that a negative worth addressing, in an effort to fix the problem even if we don't yet know exactly the functions of each kind of microbe in the community.
 

Randy Holmes-Farley

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I guess I see two categories here - results that are clearly negative (pathogens of fish or corals), and results that deviate from the typical profile. The latter deserve a separate category because there is little evidence (or in many cases, none) that these deviations are harmful, but many of us would still be interested to learn about these deviations.

Clearly negative
I've detected a known fish pathogen and a known coral pathogen each in multiple tanks (1/8 and 1/10 tanks respectively, last time I counted). There are dozens of other known pathogens in the database that are known to occur in aquariums, that I screen for but have not detected yet.

Deviations from typical levels
In terms of deviations from typical levels, its hard to ignore the variation in nitrifying microbes. I think its a complicated subject for a lot of reasons, and I do not consider low (or even undetectable) nitrifying microbes to be necessarily a problem, on their own. Most tanks have measurable ammonia-oxidizing microbes, although at a wide range of levels. A surprising number of tanks lack measurable levels of nitrite oxidizing microbes.

If the system has another mode of dealing with ammonia (e.g. macroalgae), and has no problems maintaining nutrients at the desired levels, this is probably not a problem. There are successful tanks running like that, and why change what's working? But if a tank has no other major competition for nitrogenous wastes, and is struggling with either nutrient levels or algal growth resulting from those levels, low levels of nitrifying microbes suggest a deficiency that can be addressed.

Diversity... if I remember correctly you are not convinced that low diversity is a problem that needs to be addressed, and I agree that most or maybe all of the major questions in this area have not been answered yet. But I'll point out that the starting diversity of a tank is very low, and it remains low for a long time unless we do something to change that. Many of the practices that reef keepers have found to be effective ways of adjusting the ecosystems in their aquariums (including live rock, carbon dosing, and a wide variety of bottled products with undisclosed ingredients) work by manipulating the microbial community, including its diversity. It seems clear that the microbial community is important to the health of our tanks, and diversity is one statistic describing that community.

I'd rather my tank had a diversity more like a thriving reef tank, and less like a brand tank filled with shiny white rocks. I'd consider very low diversity a negative, while acknowledging there are a range of opinions on this (like Mg or alkalinity)

If the composition of the microbial community is very different from the typical tank, I consider that a negative unless the tank has no problems. Balance scores are not intended as a value judgement (bad or good), they're a statistic describing similarity or difference with the typical community.

About half the tanks I sample fall into a cluster of similar communities. Across different users and locations. Meanwhile, other tanks (in some cases other tanks run by the same person) differ from this consensus. Some of those tanks are doing great (although if you talk to their owners, you often find out that they do something very different in their tanks than the average reef keeper). Many are not.

If the tank has a problem without any known cause, and testing reveals that it has a weird microbial community, I consider that a negative worth addressing, in an effort to fix the problem even if we don't yet know exactly the functions of each kind of microbe in the community.

I remain unconvinced, just as I am critical of the way some icp testing companies report results and recommend changes that I sometimes consider useless.
Perhaps some day we will have enough data to correlate bacteria with good vs bad. But I don’t think we are there yet, especially for profiles that are just different. Maybe different is better, not worse.
 

lexinverts

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I remain unconvinced, just as I am critical of the way some icp testing companies report results and recommend changes that I sometimes consider useless.
Perhaps some day we will have enough data to correlate bacteria with good vs bad. But I don’t think we are there yet, especially for profiles that are just different. Maybe different is better, not worse.

With respect, I'll remind everyone here that @Randy Holmes-Farley is a chemist with no training in biology, and, as far as I can tell, not much understanding regarding the research on biodiversity in the field of marine ecology. I do value Randy's skepticism very much regarding ICP testing companies recommending adjusting the levels of minor elements (based on tests of dubious accuracy), since he is an expert in reef chemistry after all. However, his blanket skepticism regarding whether microbial diversity is something we should be measuring or what it even means as a parameter, is not an expert opinion.

Randy, it sounds like you think that AquaBiomics should just hang it up now, without continuing to collect data on this new parameter. Isn't one of your complaints that we just don't have enough data yet? :rolleyes:

I think it's time that we had a microbiology forum here on Reef2Reef, so these discussions could occur in a more appropriate place without annoying Randy so much :)
 

Randy Holmes-Farley

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With respect, I'll remind everyone here that @Randy Holmes-Farley is a chemist with no training in biology, and, as far as I can tell, not much understanding regarding the research on biodiversity in the field of marine ecology. I do value Randy's skepticism very much regarding ICP testing companies recommending adjusting the levels of minor elements (based on tests of dubious accuracy), since he is an expert in reef chemistry after all. However, his blanket skepticism regarding whether microbial diversity is something we should be measuring or what it even means as a parameter, is not an expert opinion.

Randy, it sounds like you think that AquaBiomics should just hang it up now, without continuing to collect data on this new parameter. Isn't one of your complaints that we just don't have enough data yet? :rolleyes:

I think it's time that we had a microbiology forum here on Reef2Reef, so these discussions could occur in a more appropriate place without annoying Randy so much :)

with respect, that’s bunk.

I have a degree in biology from Cornell.

I have led multiple teams in antimicrobial research at multiple companies. I have patents on antimicrobial polymers. I personally lead the in vivo activities at my current company. I recently sent in a grant application I wrote entirely myself for the DOD relating to antimicrobial research that they liked enough to move to the next stage.

if that does not suffice to allow me to give an opinion on bacteria without someone trashing my background, then I would suggest we should limit participation in chemistry discussions in this chemistry forum to the seven people who frequent this forum with advanced degrees in chemistry.

But no, we allow everyone to participate. Folks who think a statement is wrong need to focus on the statement, not who said it or what their background is. I do that all the time for folks making ridiculous statements. I focus only on the statement, not the person making it.

Don’t put words in my mouth. I have expressed skepticism of the ability to look at bacteria results and say what is good and what is not. If you think you can, you are either far smarter than me, or deluding yourself. I did not say the research is not worth doing. Never have. But if you want me to stick to a chemical analogy that you seem to think I know more about, it would be like an icp test being used to say good or bad without even knowing what is present in seawater. It is well worth the study.

But It may be a long time before it can suggest corrective actions of clear benefit.
 

Randy Holmes-Farley

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With respect, I'll remind everyone here that @Randy Holmes-Farley I think it's time that we had a microbiology forum here on Reef2Reef, so these discussions could occur in a more appropriate place without annoying Randy so much :)

I’m sure it would be more fun to have only certified true believers allowed to participate.
 

lexinverts

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with respect, that’s bunk.

I have a degree in biology from Cornell.

I have led multiple teams in antimicrobial research at multiple companies. I have patents on antimicrobial polymers. I personally lead the in vivo activities at my current company. I recently sent in a grant application I wrote entirely myself for the DOD relating to antimicrobial research that they liked enough to move to the next stage.

if that does not suffice to allow me to give an opinion on bacteria without someone trashing my background, then I would suggest we should limit participation in chemistry discussions in this chemistry forum to the seven people who frequent this forum with advanced degrees in chemistry.

But no, we allow everyone to participate. Folks who think a statement is wrong need to focus on the statement, not who said it or what their background is. I do that all the time for folks making ridiculous statements. I focus only on the statement, not the person making it.

Don’t put words in my mouth. I have expressed skepticism of the ability to look at bacteria results and say what is good and what is not. If you think you can, you are either far smarter than me, or deluding yourself. I did not say the research is not worth doing. Never have. But if you want me to stick to a chemical analogy that you seem to think I know more about, it would be like an icp test being used to say good or bad without even knowing what is present in seawater. It is well worth the study.

But It may be a long time before it can suggest corrective actions of clear benefit.



You see, since you have summarily dismissed all of the Aquabiomics detailed responses to your skepticism with glib, dismissive statements, it does seem like you know very little about the field of microbial ecology. Perhaps you should actually engage with the arguments put forward by AquaBiomics instead of your tiresome "listen to the expert" types of responses. That may fly when you are discussing reef chemistry, but not for marine microbial ecology.

I'm not saying that you shouldn't post here (in your own forum...LOL), I'm just pointing out to people who view you as an expert in this section of Reef2Reef, that some of these posts regarding biodiversity of reef aquaria are not the same level of quality as your chemistry posts. :)
 
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lexinverts

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I’m sure it would be more fun to have only certified true believers allowed to participate.

It would be more fun to post about reef tank microbial biology in a portion of reef2reef that was dedicated to reef tank microbial biology, rather than in the chemistry section. I guess if you don't see the difference between reef tank microbial biology and reef tank chemistry, you have made my previous point for me. :)
 

Randy Holmes-Farley

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Perhaps you should actually engage with the arguments put forward by AquaBiomics instead of your tiresome "listen to the expert" types of responses.

I think I have been very even handed in allowing a company to boost their services here in this forum because they are adding useful info to the discussion. But that comes with the expectation that I am going to challenge assertions that lack supporting evidence.

The main thing I have expressed a problem with (aside from details relating to things like benthic bacteria verses suspended) is the assumption that higher diversity of bacteria is better.

Do you claim to have an adequate understanding of the issues involved to provide a clear reason why and when higher diversity is better in a reef tank than lower diversity, and what the data supporting that assertion is?
 
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lexinverts

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I think I have been very even handed in allowing a company to boost their services here in this forum because they are adding useful info to the discussion. But that comes with the expectation that I am going to challenge assertions that lack supporting evidence.

The main thing I have expressed a problem with (aside from details relating to things like benthic bacteria verses suspended) is the assumption that higher diversity of bacteria is better.

Do you claim to have an adequate understanding of the issues involved to provide a clear reason why and when higher diversity is better in a reef tank than lower diversity, and what the data supporting that assertion is?

Other than divulge that I have a PhD in Ecology, I'm going to sign out of this discussion. I made my point, and AquaBiomics has already provided numerous detailed answers to your questions, and you have mostly ignored them. :)
 

Randy Holmes-Farley

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Other than divulge that I have a PhD in Ecology, I'm going to sign out of this discussion. I made my point, and AquaBiomics has already provided numerous detailed answers to your questions, and you have mostly ignored them. :)

I haven’t ignored anything in this thread. What their statements lack is a clear statement of exactly when and how higher diversity has a benefit that reefers can recognize.
 

lexinverts

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I haven’t ignored anything in this thread. What their statements lack is a clear statement of exactly when and how higher diversity has a benefit that reefers can recognize.

For the sake of the observers of this discussion, I am providing a list of scientific papers that do present the case for the importance of species richness in pretty much any ecosystem that has been studied to date. (This is the same list that AquaBiomics provided to Randy in a previous thread, and is as good as any list that I could pull together.)

References:
1. Naeem, S., Thompson, L., Lawler, S. et al. Declining biodiversity can alter the performance of ecosystems. Nature 368, 734–737 (1994)
2. Duffy JE, Godwin CM, Cardinale BJ. 2017. Biodiversity effects in the wild
are common and as strong as key drivers of productivity
. Nature 549:261–264.
3. Isbell F, Craven D, et al. (2015). Biodiversity increases the resistance of ecosystem productivity
to climate extremes
. Nature 526:574 –577.
4. Weber, L., González‐Díaz, P., et al. (2019), Microbial signatures of protected and impacted Northern Caribbean reefs: changes from Cuba to the Florida Keys. Environ Microbiol.

It's hard to ignore meta-analyses published in Nature on the importance of species richness across all types of ecosystems in nature, including reef ecosystems. Yes, it usually is better (in a wide range of ways) to have higher species richness. Our reef tanks are artificial ecosystems, but ecosystems nonetheless. Based on the above exhaustive research, it's a reasonable starting assumption that our reef tanks will not be completely different from nature, just like we don't expect the rules of water chemistry to be completely different in our tanks from what we observe in natural reefs.

The straw man that is being batted about in this thread (and others) like a piñata is the notion that someone has said that "higher diversity" is always the best, or that we already know exactly what the "ideal microbiome" is for a reef tank. I know that AquaBiomics has never said that. He has been extremely careful in the interpretation of his results not to overstate anything. He has never claimed to be offering a "black and white" type of prescription for reef tank problems. What he can do is make recommendations based on the data that he has thus far, and this goes beyond what many reef product companies can honestly say about their services...

The exciting thing about this effort is that we are learning more every time Eli completes the analysis of another data set. In this other thread, a well known hobbyist here (Reefnjunkie) reports his AquaBiomics results. His results are interesting because he lost almost everything from the system documented here to RTN and STN. (Many of you will recognize this as one of the most epic sps collections ever photographed.) It turns out that he had an undescribed strain of Vibrio that made up 5% of the bacterial community in the sps system that crashed and it has only been found in one other system, which also reported STN. Did Reefnjunkie's system have an unhealthy/different microbiome that in some way allowed a pathogenic Vibrio strain to persist when it was introduced, and then eventually take over? As long as we keep collecting these data, we will get closer to answers like these. :)
 

lexinverts

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From your analysis of those papers, in what scenario would you suggest that increasing diversity of bacterial species will have an apparent benefit to a reef tank?

Sure, if you are having trouble with nuisance algae or if you are having issues with STN or RTN, and your AB species richness score or balance score is out of line with the majority of tanks studied, it may help to add some new live rock or live sand. Just like microbial competition keeps our own guts in balance, microbial competition among species keeps natural ecosystems in balance, and this may very well extend to the ecosystems in our reef tanks.

You can see the immediate effect of addition of live sand to the microbiome in the AquaBiomics tanks here:


I am currently trying this same treatment on one of my tanks that is suffering from a dinoflagellate problem.
 

Randy Holmes-Farley

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Sure, if you are having trouble with nuisance algae or if you are having issues with STN or RTN, and your AB species richness score or balance score is out of line with the majority of tanks studied, it may help to add some new live rock or live sand. Just like microbial competition keeps our own guts in balance, microbial competition among species keeps natural ecosystems in balance, and this may very well extend to the ecosystems in our reef tanks.

You can see the immediate effect of addition of live sand to the microbiome in the AquaBiomics tanks here:


I am currently trying this same treatment on one of my tanks that is suffering from a dinoflagellate problem.

If the future data bear out that hypothesis between diversity and algae, that will be very interesting.

I think one could equally well suggest that, if there is a bacterial component, that specific species provide the benefit, not the number of different species present. Adding those species could be beneficial if they are lacking, while increasing other species may not be. Thus my concern that diversity is perhaps an overly course tool for these sorts of hypotheses.
 

lexinverts

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If the future data bear out that hypothesis between diversity and algae, that will be very interesting.

I think one could equally well suggest that, if there is a bacterial component, that specific species provide the benefit, not the number of different species present. Adding those species could be beneficial if they are lacking, while increasing other species may not be. Thus my concern that diversity is perhaps an overly course tool for these sorts of hypotheses.

Yes, this is a valid point. This is why the AquaBiomics reports include a species richness score and, both include a profile of the identity of the species present, and provide a "balance" score, which compares your microbial community to the most commonly reported community compositions. If a thriving sps tank had a low species richness score, and a low balance score that could indicate the presence of a particularly effective reef tank community.

As the database is built for the core microbiome, we will learn more and more about the ideal microbial community composition, and the potential importance of unique communities.
 

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One thing I think would be interesting to see is a before/after of the same tank involving so called reef safe treatments/additives. I would like to see the consequence(if any) on the populations in a tank after treating with Vibrant, Chemiclean, Reef Rally etc... Not saying I wouldn't still use one if I felt the need but it's always nice to have a clearer picture of the consequences of our choices.
 

AquaBiomics

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One thing I think would be interesting to see is a before/after of the same tank involving so called reef safe treatments/additives. I would like to see the consequence(if any) on the populations in a tank after treating with Vibrant, Chemiclean, Reef Rally etc... Not saying I wouldn't still use one if I felt the need but it's always nice to have a clearer picture of the consequences of our choices.
Absolutely. Just finished sampling one experiment with some bacterial additives, and I may do Vibrant and similar products next.

If two different products have basically the same effects (or ingredients), if two different products each affect a different group of microbes, that would be nice to know, or if the benefit of a product depends on the existing community, that would be nice to know.
 

Nano sapiens

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Hi Eli - Wondering if you might have test results from a healthy reef in nature. Would be interesting to compare with our captive reef systems.

I took a stroll around the Web and found this fascinating paper directly in line with the question 'What does a healthy, natural reef water column microbial community look like?'

https://www.nature.com/articles/s41467-019-09419-z

This research deals specifically with the microbial communities on four of the Southern Line Islands (some of the most pristine coral reef communities in the world). Not only the composition of the microbial community is determined (some interesting microbial differences from our reef systems stand out), but it also answers the question of how does the microbial community differ in a 24 hr period? Turns out, the difference is 'day and night', literally! The daytime community makeup is quite different from the one at night. In fact, the difference is more pronounced from day to night in one specific spot than from one island to another island.

I think it's safe to presume that the day and night microbiome in our reef systems also undergoes a day-to-night change. Would the changes be as pronounced? More pronounced? How would the microbial families makeup/percentages be different at night vs. day?

Interesting stuff!

Ralph.
 

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