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

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lexinverts

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Which are you - a salesman or a scientist. There is at least data behind ICP testing (though perhaps not behind individual testing companies)? I mean - it was a snappy reply - but it didnt answer what I asked - which was - along the lines of - one of my tanks is having a problem - Is there a charge for sending in a sample. It seems to (me) that a scientist would consider this a valuable piece of data.
He's a scientist who is running a DNA sequencing business for the aquarium hobby.
I think he did answer your question. "DNA sequencing isn't free."
 

AquaBiomics

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Which are you - a salesman or a scientist. There is at least data behind ICP testing (though perhaps not behind individual testing companies)? I mean - it was a snappy reply - but it didnt answer what I asked - which was - along the lines of - one of my tanks is having a problem - Is there a charge for sending in a sample. It seems to (me) that a scientist would consider this a valuable piece of data.
Sorry if it came across as snappy. I tried to lay out the prices clearly on the website so I guess on my first reading I didn't interpret it as a question in search of an answer -- my bad. To answer your question, I have discounts in place up to 3 samples and can definitely discount further for additional samples. I'll add details to the site about that, its a good point. I'd be happy to discuss in PM or emails.

And while I have plenty of training in science I confess to having none in sales, which I imagine shows :)
 

Nano sapiens

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I believe that we are in for some very interesting surprises as this progresses. Just these two examples from Scubabum and Scott Campbell raise all kinds of questions regarding what conditions favor the relative dominance of one type of bacteria/archea over another, even if they perform the same relative function in a system.

The way I look at it, for the price of a nice frag a test to determine the makeup of my tank's microbiome is well worth it :)
 

AquaBiomics

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Ok as promised here are the results of my AquaBiomics test on my 26 year old 58 gallon Reef tank. Received my results on week 5.. This data provides detailed information on the community of microbes living in my aquarium. Each type of microbe in my sample was identified by comparing DNA sequences from my sample with a database of DNA sequences from known types. The relative abundance of each sequence can be used to compare the relative abundance of each type across samples. Looks like the diversity of my tanks Microbiome is lower than than typical range. I'll be the first to admit I don't know what most of this information means but looking forward to hearing comments of those that do.

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Hi Scubabum,

Thanks for sharing your results! Here are my thoughts on your tank's microbiome and how it compares to others, from the perspective of someone who has spent a bunch of time recently looking at aquarium microbiomes.

Your diversity is lower than many but it's not unusual. I included the percentile scale to put some numbers on this... about 2/3 of tanks are more diverse than yours, and about 1/3 are lower. I find it very interesting that a tank established so long is in the lower half of diversity - its consistent with the idea that diversity declines over time as some bugs outcompete others. But still, if you value diversity, rest assured there are plenty of tanks with lower scores.

The balance of your microbial community, on the other hand, is very different than the typical reef tank. In other words, while your tank has the expected kinds of microbes, they are present at very different levels than the typical reef tank. The score (0.08) indicates this, and the barplot (part 2) shows it graphically. Notice that your tank has a ton of Oceanospirillaceae (which is typically rare), and very little Flavobacteriaceae or Pelagibacteraceae (which are typically very abundant).

If you refer to my description of these families (available on the AquaBiomics site) you can read more about the activity of these groups. I am personally struck by the differences in nutritional requirements...

Your tank has high levels of ammonia-oxidizing microbes (all Archaea in your case rather than Bacteria), but low levels of nitrite-oxidizing microbes. Since your biofilm sample produced high quality data, this isnt for lack of sampling. Your tank is not alone in this respect. NOB are always less abundant (perhaps 20-fold) than AOB, but they also vary a lot among tanks.

I want to be clear that I do not interpret this as proof they're absent. I'm sure they are present, in a 20+ year old tank. But this shows the NOB population is low relative to many other tanks. Which I see more often than I would have suspected.

Your tank appears free of specific problematic microbes like cyanobacteria, or pathogens or fish or corals. Many tanks in this round had high cyano levels, a few had fish pathogens, none had coral pathogens.

Is that useful?
 
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Scubabum

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Hi Scubabum,

Thanks for sharing your results! Here are my thoughts on your tank's microbiome and how it compares to others, from the perspective of someone who has spent a bunch of time recently looking at aquarium microbiomes.

Your diversity is lower than many but it's not unusual. I included the percentile scale to put some numbers on this... about 2/3 of tanks are more diverse than yours, and about 1/3 are lower. I find it very interesting that a tank established so long is in the lower half of diversity - its consistent with the idea that diversity declines over time as some bugs outcompete others. But still, if you value diversity, rest assured there are plenty of tanks with lower scores.

The balance of your microbial community, on the other hand, is very different than the typical reef tank. In other words, while your tank has the expected kinds of microbes, they are present at very different levels than the typical reef tank. The score (0.08) indicates this, and the barplot (part 2) shows it graphically. Notice that your tank has a ton of Oceanospirillaceae (which is typically rare), and very little Flavobacteriaceae or Pelagibacteraceae (which are typically very abundant).

If you refer to my description of these families (available on the AquaBiomics site) you can read more about the activity of these groups. I am personally struck by the differences in nutritional requirements...

Your tank has high levels of ammonia-oxidizing microbes (all Archaea in your case rather than Bacteria), but low levels of nitrite-oxidizing microbes. Since your biofilm sample produced high quality data, this isnt for lack of sampling. Your tank is not alone in this respect. NOB are always less abundant (perhaps 20-fold) than AOB, but they also vary a lot among tanks.

I want to be clear that I do not interpret this as proof they're absent. I'm sure they are present, in a 20+ year old tank. But this shows the NOB population is low relative to many other tanks. Which I see more often than I would have suspected.

Your tank appears free of specific problematic microbes like cyanobacteria, or pathogens or fish or corals. Many tanks in this round had high cyano levels, a few had fish pathogens, none had coral pathogens.

Is that useful?
Thank you for the explanation. Very useful. I'm always looking to explore and learn new things in the hobby I've loved so much over the the last 26 years. Testing like this can only benefit and help us understand and learn new things in the hobby. I often think of how far things have evolved since when I started almost 3 decades ago. Thank you.
 

MnFish1

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He's a scientist who is running a DNA sequencing business for the aquarium hobby.
I think he did answer your question. "DNA sequencing isn't free."
Not going to debate what he said/meant or what I said/meant. IMHO its a solution in search of a problem which is being funded by people who 'are interested' - which is all good. I'm not sure why you're calling me out. it is my opinion. I asked how much 6 tests would cost? maybe you missed that?
 

MnFish1

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Sorry if it came across as snappy. I tried to lay out the prices clearly on the website so I guess on my first reading I didn't interpret it as a question in search of an answer -- my bad. To answer your question, I have discounts in place up to 3 samples and can definitely discount further for additional samples. I'll add details to the site about that, its a good point. I'd be happy to discuss in PM or emails.

And while I have plenty of training in science I confess to having none in sales, which I imagine shows :)
Thanks - Appreciated - PM me with the price for 6 tests. Thanks again for politely answering - and don't take anything I've said as a personal criticism (of you) - But merely a question of your product and its usefulness to 'me'.
 

lexinverts

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Not going to debate what he said/meant or what I said/meant. IMHO its a solution in search of a problem which is being funded by people who 'are interested' - which is all good. I'm not sure why you're calling me out. it is my opinion. I asked how much 6 tests would cost? maybe you missed that?
It seemed pretty clear to me you were suggesting that if he wasn't doing tests for free that he wasn't a scientist, so I cleared that up for you. You also said that you wouldn't pay for the service. Then you asked how much it would cost. Honestly, it is hard to keep up with the volume of your posts and their sometimes rapidly shifting meaning.
 

MnFish1

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It seemed pretty clear to me you were suggesting that if he wasn't doing tests for free that he wasn't a scientist, so I cleared that up for you. You also said that you wouldn't pay for the service. Then you asked how much it would cost. Honestly, it is hard to keep up with the volume of your posts and their sometimes rapidly shifting meaning.
Sorry - please feel free to ignore them:)
 
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Scott Campbell

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Hi Scubabum,

Thanks for sharing your results! Here are my thoughts on your tank's microbiome and how it compares to others, from the perspective of someone who has spent a bunch of time recently looking at aquarium microbiomes.

Your diversity is lower than many but it's not unusual. I included the percentile scale to put some numbers on this... about 2/3 of tanks are more diverse than yours, and about 1/3 are lower. I find it very interesting that a tank established so long is in the lower half of diversity - its consistent with the idea that diversity declines over time as some bugs outcompete others. But still, if you value diversity, rest assured there are plenty of tanks with lower scores.

The balance of your microbial community, on the other hand, is very different than the typical reef tank. In other words, while your tank has the expected kinds of microbes, they are present at very different levels than the typical reef tank. The score (0.08) indicates this, and the barplot (part 2) shows it graphically. Notice that your tank has a ton of Oceanospirillaceae (which is typically rare), and very little Flavobacteriaceae or Pelagibacteraceae (which are typically very abundant).

If you refer to my description of these families (available on the AquaBiomics site) you can read more about the activity of these groups. I am personally struck by the differences in nutritional requirements...

Your tank has high levels of ammonia-oxidizing microbes (all Archaea in your case rather than Bacteria), but low levels of nitrite-oxidizing microbes. Since your biofilm sample produced high quality data, this isnt for lack of sampling. Your tank is not alone in this respect. NOB are always less abundant (perhaps 20-fold) than AOB, but they also vary a lot among tanks.

I want to be clear that I do not interpret this as proof they're absent. I'm sure they are present, in a 20+ year old tank. But this shows the NOB population is low relative to many other tanks. Which I see more often than I would have suspected.

Your tank appears free of specific problematic microbes like cyanobacteria, or pathogens or fish or corals. Many tanks in this round had high cyano levels, a few had fish pathogens, none had coral pathogens.

Is that useful?
Eli

Any thoughts as to what the "consequences" of having a tank with very little Flavobacteriaceae and/or Pelagibacteraceae might be? In other words - do these particular bacteria perform a uniquely valuable role and their absence in a tank (like mine <lol>) might be worrisome? Or do all these major strains of bacteria largely overlap each other in function?

And do you think the organisms growing in the tank (coral, algae, sponges) over time control and shape the bacterial ratios and these organisms may simply have no need or preference for certain bacterial strains? To a degree that certain bacterial strains are eventually not supported by the life in the tank. Or do you think the existing bacterial colonies themselves determine which higher level organisms thrive or perish? And the ratios are then determined by which bacterial colony can achieve dominance over time based on lighting, food input, water movement and other tank parameters - regardless of the higher organisms living in the tank. Or maybe both possibilities?

Basically wondering if my tank has low bacterial diversity because that is the "preference" of the corals, algae and sponges that have been in my tank for so long. Or if it is because the diversity of my tank is slowly degrading over time as certain strains basically go extinct in my tank.

Fascinating stuff. Thank you for doing this!

Scott
 

lexinverts

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Eli

Any thoughts as to what the "consequences" of having a tank with very little Flavobacteriaceae and/or Pelagibacteraceae might be? In other words - do these particular bacteria perform a uniquely valuable role and their absence in a tank (like mine <lol>) might be worrisome? Or do all these major strains of bacteria largely overlap each other in function?

And do you think the organisms growing in the tank (coral, algae, sponges) over time control and shape the bacterial ratios and these organisms may simply have no need or preference for certain bacterial strains? To a degree that certain bacterial strains are eventually not supported by the life in the tank. Or do you think the existing bacterial colonies themselves determine which higher level organisms thrive or perish? And the ratios are then determined by which bacterial colony can achieve dominance over time based on lighting, food input, water movement and other tank parameters - regardless of the higher organisms living in the tank. Or maybe both possibilities?

Basically wondering if my tank has low bacterial diversity because that is the "preference" of the corals, algae and sponges that have been in my tank for so long. Or if it is because the diversity of my tank is slowly degrading over time as certain strains basically go extinct in my tank.

Fascinating stuff. Thank you for doing this!

Scott
Is declining microbial diversity with time related to “old tank syndrome?” Lots of interesting questions!
 

Nano sapiens

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Is declining microbial diversity with time related to “old tank syndrome?” Lots of interesting questions!
I was thinking along similar lines. It stands to reason that a system that relies on a much reduced set of bacteria/archaea species would be more prone to collapse if the dominant genus/genera were greatly reduced (or even disappear) for some reason. In a highly diversified system there would be more actors to 'fill in the blanks', so to speak. All in theory, of course :)
 

Nano sapiens

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Speaking of OTS, I was pondering all the events that a 20 yr, 30 yr or older aquarium could go through from heater malfunction resulting in critical high or low temperatures, accidental overdosing with chemicals, freshwater flooding from a malfunctioning ATO, the odd bolt, screw or nut falling in unnoticed for an extended period of time, cracked magnet casings and the resulting corrosion, little Johnny throwing a bar of soap in the tank...and I can think of a few more. A series of these events over time could cause a permanent bacteria/archaea community reorg and/or a reduction in the overall diversity of the microbiome community.
 
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Speaking of OTS, I was pondering all the events that a 20 yr, 30 yr or older aquarium could go through from heater malfunction resulting in critical high or low temperatures, accidental overdosing with chemicals, freshwater flooding from a malfunctioning ATO, the odd bolt, screw or nut falling in unnoticed for an extended period of time, cracked magnet casings and the resulting corrosion, little Johnny throwing a bar of soap in the tank...and I can think of a few more. Any of these events could cause a permanent bacteria/archaea community reorg and/or a reduction in the overall diversity of the microbiome community.
Those events could diminish the amounts of bacteria, but most likely not decimate them. In time they would likely recover.
 

lexinverts

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Speaking of OTS, I was pondering all the events that a 20 yr, 30 yr or older aquarium could go through from heater malfunction resulting in critical high or low temperatures, accidental overdosing with chemicals, freshwater flooding from a malfunctioning ATO, the odd bolt, screw or nut falling in unnoticed for an extended period of time, cracked magnet casings and the resulting corrosion, little Johnny throwing a bar of soap in the tank...and I can think of a few more. Any of these events could cause a permanent bacteria/archaea community reorg and/or a reduction in the overall diversity of the microbiome community.
It's like genetic drift, but with the microbial community. Unless you are right by the ocean and are getting new colonists via the air, or you are adding new live rock frequently, your microbial diversity goes down with time.
 
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Nano sapiens

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Those events could diminish the amounts of bacteria, but most likely not decimate them. In time they would likely recover.
I agree that the total count of bacteria would recover, but those bacteria that were most severely affected by an event/events might not be able to regain their previous abundance and some could possibly die out completely.
 
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I agree that the total count of bacteria would recover, but those bacteria that were most severely effected by an event/events might not be able to regain their previous abundance and some could possibly die out completely. All conjecture, of course, but I can imagine that the battle for bacterial dominance is just as intense as the battle we see with organisms fighting for space/dominance on the reef.
Theoretically yes.

I'm in the group that has a limited bacterial diversity. I'm considering adding bottled bacteria and some live rock from the ocean.

Starting with the majority of my rock as dry rock, the rest was from a long term established system. Conjecture speaking, diversity waned either over time or wasn't there to begin with.
 

Nano sapiens

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Theoretically yes.

I'm in the group that has a limited bacterial diversity. I'm considering adding bottled bacteria and some live rock from the ocean.

Starting with the majority of my rock as dry rock, the rest was from a long term established system. Conjecture speaking, diversity waned either over time or wasn't there to begin with.
Ultimately, I think we'll find that there are multiple reasons for the loss of biodiversity in older systems. What will be interesting is finding a 20 or 30 year old system that doesn't regularly add bacterial sources and yet has very high bacterial biodiversity. If this exists, that'll be one to study in depth!
 
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Ultimately, I think we'll find that there are multiple reasons for the loss of biodiversity in older systems. What will be interesting is finding a 20 or 30 year old system that doesn't regularly add bacterial sources and yet has very high bacterial biodiversity. If this exists, that'll be one to study in depth!
Very much so. The dynamics of that tank, every aspect would need to be disclosed In full detail.
 
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