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FAQ / what interesting things does aquabiomics now know/believe?
I was stuck on a long solo drive recently, so I listened to a handful of talks, interviews and Q&As that Eli Meyer of aquabiomics has given in the last year and pulled out all the interesting (to me) bits that he now knows or believes based on looking back at a couple of years of hobby data.
These are the points I found interesting, and most are semi-relevant to this discussion.
Q1: what’s the typical community composition based on? / How similar to a real reef is it?
linkQ1
The picture of the “average” tank is based on hobby - not wild reefs, because hobby tank microbiomes look very unlike real reefs.
First - the pic of typical tank is based on all the tanks in the database that are “normal” reef tanks - not experimental, not aquaculture facilities, not tanks with any bad health issues, die-offs, nor any tanks where the sampling might have given low quality data. Beyond that it’s the average of the hobby. And the hobby shows clear repeatable dominant families - which are used to mark the balance score.
Q2 how is hobby “typical” different from Real reefs?
linkQ2
Real reefs are most dominated by 3 groups in the water: the largest is pelagibacteraceae, and then 2 kinds of single cell tiny planktonic cyanobacteria.(I think this is a reference to Synechococcus and Prochlorococcus). Hobby tanks can have the pelagibacteraceae as a major component, but they are true water-living types, so UV makes them disappear.
Q3 Does ____ affect bacterial diversity or the overall bacterial community enough to care about?
a) live rock: Some does - some doesn’t
LinkQ3a
Eli believes only dead coral skeleton is actually the correct material to provide the right microbial community. Some live rock looks very diverse - covered with life but in testing it didn’t create bacterially diverse system, and was solid inside. Live rock rubble that was actual porous dead coral skeleton did repeatably create bacterially diverse system in only 4 weeks, although it wasn’t as impressively “alive” visibly.
b) corals: huge coral with a stony base - probably. Coral frags - probably not
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.
d) Carbon dosing?
linkq3d
Carbon dosing generally boosts 3 families: Alteromonadaceae, Fusobacteriaceae, and Oceanospirilliaceae. These 3 are families normally present, but carbon dosing increases their proportions. It’s not yet known which carbon sources experimentally drive which families, but if you carbon dose one or more of them, will bloom in large numbers.
Also, carbon dosing tanks tend to have low nitrifying communities, as the heterotrophic uptake of carbon also causes competition for ammonia.
e) bottled bacterial products
linkq3e
“There’s always a very short list of [bacterial] ingredients, 2 or 3 - maybe some might have 7. Almost none of those seem to persist very long in the aquarium.” and even if they all did, that small number of types would do almost nothing for measured diversity.
linkQ3e2
“The components of bottled bacterial products are not the components of a reef tank microbiome, in a venn diagram there’s little intersection between those two circles. The viewer can interpret that how they wish.”
These products DO have an effect on the microbiome of the tank. These effects are seen over and over. If you dose most bottled bacterial products, you will see a bloom in the family Fusobacteriaceae (one of the families Eli has said increase from carbon dosing). But this family is not a component of the bottled products. A lot of the effects that we see from bottled products probably come from the addition of nutrients in the bottles that feed bacteria resident in the tank already.
It seems they are selecting bacteria for the bottles intended for a specific purpose “consuming ammonia” “degrading polysaccharides form algal cell walls” but having those bacteria become part of the ongoing community is not an expectation and it doesn’t seem to happen.
Eli says he thinks they are overused in the hobby and adding to an established tank is probably not a sensible use of the products.
f) macroalgae fuge:
linkQ3f
No statistical difference in overall diversity in systems with/without fuges. Some major groups are affected, though. Flavobacteraceae are known from literature to be algal-surface associated, and they are measured to be higher in many tanks with macroalgae. Alteromonadaceae feed on carbohydrates, which are released by macroalgae, so in principle ought to be higher in systems with macroalgae (no mention if measured data supports that).
g) mixed reef vs SPS:
Don’t know if one is more diverse than another. No data.
h) barebottom vs sandbed
linkQ3h
No statistical difference found, but Eli believes that there wasn’t enough data and with more sandbed data - tanks with sandbeds will show more diversity than barebottom. There is a different microenvironment in the sand, so communities ought to be different. Sand has types of microbes not present in the water and/but… the diversity of aquarium sand itself is often kind of low - because sand contains big biofilms that are basically just one type.
i) skimmer?
linkQ3i
Tanks with skimmers still record good levels of pelagibacteraceae ( the most common bacteria in the water on real reefs), so it is not dangerously efficient at removing typical bacteria. Unlike UV, which can be dangerously efficient.
linkQ3i2
Hard to answer definitive statistical differences with/without skimmer, because the database of people with no skimming is so small.
j) UV ?
linkQ3j
UV strongly removes the single family common to tanks that is the most prevalent on real reefs - pelagibacteraceae. The effect is so strong that Eli can tell if your UV bulb needs replacing by whether you are running UV and still have this family. For that reason Eli likes to caution against running UV for no reason. But he always mentions that there are plenty of healthy coral tanks with UV, so it’s not an absolute need to have this group.
k) Trace elements?
LinkQ3k
Don’t know. No data on it, but the expectation from literature is that Iron certainly will. Other minor components of seawater may also.
Q4 if corals are having issues, should you check the bacteria?
LinkQ4
1st, check chemistry parameters yourself. 2nd, check ICP. 3rd then look at bacteria if no answers from the others. .
Q5 Do established tanks that are tested repeatedly show stable consistent results, or constant changes?
linkQ5
They will often test very stable month after month, and then something (a disturbance) changes and the microbiome will be totally different. These might represent nutrient shifts.
Q6 Have you tested ____ bacterial product, will you write an article?
LinkQ6
They’ve tested a bunch of products. Probably not going to be an article. He decided that making a bunch of companies mad was not a great business strategy to start with. But he is happy to run tests on products for any hobbyist who wants to know and share - he’s just not going to write an article listing the bacterial ingredients in all the hobby products.
Q7 Are some bacteria only in water, and others only on surfaces?
LinkQ7
Although some groups grow on surfaces, they are easily measured in the water. Likewise groups that live in the water are measured on surfaces. These distinctions aren’t absolutes, and the same applies to nitrifiers.
Q8 What coral pathogens are detected in the hobby?
LinkQ8
Of nine suspected pathogens responsible for Stony Coral Tissue Loss Disease, four are found in the hobby, with a couple of them in 20% of tanks. (the strongest candidate - in 100% of wild diseased corals, was in 3% of hobby tanks.) It’s impossible to know if these pathogens affect our corals because we are mixing pathogens from the caribbean with corals that aren’t from the caribbean. So they would never meet in nature, thus there’s no data on them.
There’s also an R2R thread on aquabiomics nailing down Brown Jelly Disease to one particular bacteria.
Q9 how does diversity trend over time?
LinkQ9
Tanks over time (years) tend to trend down in bacterial diversity. Avoiding this - if that’s your goal, is probably easiest done by supplementation with small occasional amounts of live sand/mud. (Be aware some bags of these products test positive for fish/coral pathogens - so it’s not an activity with no downside.)
Q10 Tank start with ammonia or ghost feeding?
LinkQ10
Ghost feeding is what Eli does. Because the community of organisms that exists on reefs and in reef tanks is large and diverse and slow to establish. Ammonia-only delays that, compared to starting with a natural food so that the rest of the community can begin maturing at the same time as the nitrifiers.
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. Corals are bombarded with bacteria on real reefs and the majority of these are pelagibacteraceae.
Q12 what group of bacteria are most closely associated with coral?
LinkQ12
Vibrio, are a group that is often thought of as concerning because it’s got many known pathogens in it, but it’s also the group that is most associated with animal surfaces like coral flesh. Coral farms can have over 50% vibrionaceae in their water samples. That doesn’t mean they have pathogens, it just means there are a lot of good and bad bacteria in that same family.
Q13 Under what situations does Eli think that live rubble and live sand/mud are useful for the bacterial community?
LinkQ13
Eli has done experiments using live reef rubble (live rock in the form of dead coral skeletons) to establish a good community to start a tank and live sand/mud to enhance a community in an established tank. Perhaps the added surface area of sand/mud makes it more useful in a system already established. But it may be that both materials are good in both situations, but the experiments are as listed above.
Q14 Do corals eat bacteria?
LinkQ14
It’s contentious among coral scientists, but there’s good evidence from radio-labeling that coral ingest nutrients from bacteria, but we have no idea what bacteria they eat. By number they encounter pelagibacteriaceae the most - but no data to say that's what they eat.
[edit: maybe links work now]
I was stuck on a long solo drive recently, so I listened to a handful of talks, interviews and Q&As that Eli Meyer of aquabiomics has given in the last year and pulled out all the interesting (to me) bits that he now knows or believes based on looking back at a couple of years of hobby data.
These are the points I found interesting, and most are semi-relevant to this discussion.
Q1: what’s the typical community composition based on? / How similar to a real reef is it?
linkQ1
The picture of the “average” tank is based on hobby - not wild reefs, because hobby tank microbiomes look very unlike real reefs.
First - the pic of typical tank is based on all the tanks in the database that are “normal” reef tanks - not experimental, not aquaculture facilities, not tanks with any bad health issues, die-offs, nor any tanks where the sampling might have given low quality data. Beyond that it’s the average of the hobby. And the hobby shows clear repeatable dominant families - which are used to mark the balance score.
Q2 how is hobby “typical” different from Real reefs?
linkQ2
Real reefs are most dominated by 3 groups in the water: the largest is pelagibacteraceae, and then 2 kinds of single cell tiny planktonic cyanobacteria.(I think this is a reference to Synechococcus and Prochlorococcus). Hobby tanks can have the pelagibacteraceae as a major component, but they are true water-living types, so UV makes them disappear.
Q3 Does ____ affect bacterial diversity or the overall bacterial community enough to care about?
a) live rock: Some does - some doesn’t
LinkQ3a
Eli believes only dead coral skeleton is actually the correct material to provide the right microbial community. Some live rock looks very diverse - covered with life but in testing it didn’t create bacterially diverse system, and was solid inside. Live rock rubble that was actual porous dead coral skeleton did repeatably create bacterially diverse system in only 4 weeks, although it wasn’t as impressively “alive” visibly.
b) corals: huge coral with a stony base - probably. Coral frags - probably not
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.
d) Carbon dosing?
linkq3d
Carbon dosing generally boosts 3 families: Alteromonadaceae, Fusobacteriaceae, and Oceanospirilliaceae. These 3 are families normally present, but carbon dosing increases their proportions. It’s not yet known which carbon sources experimentally drive which families, but if you carbon dose one or more of them, will bloom in large numbers.
Also, carbon dosing tanks tend to have low nitrifying communities, as the heterotrophic uptake of carbon also causes competition for ammonia.
e) bottled bacterial products
linkq3e
“There’s always a very short list of [bacterial] ingredients, 2 or 3 - maybe some might have 7. Almost none of those seem to persist very long in the aquarium.” and even if they all did, that small number of types would do almost nothing for measured diversity.
linkQ3e2
“The components of bottled bacterial products are not the components of a reef tank microbiome, in a venn diagram there’s little intersection between those two circles. The viewer can interpret that how they wish.”
These products DO have an effect on the microbiome of the tank. These effects are seen over and over. If you dose most bottled bacterial products, you will see a bloom in the family Fusobacteriaceae (one of the families Eli has said increase from carbon dosing). But this family is not a component of the bottled products. A lot of the effects that we see from bottled products probably come from the addition of nutrients in the bottles that feed bacteria resident in the tank already.
It seems they are selecting bacteria for the bottles intended for a specific purpose “consuming ammonia” “degrading polysaccharides form algal cell walls” but having those bacteria become part of the ongoing community is not an expectation and it doesn’t seem to happen.
Eli says he thinks they are overused in the hobby and adding to an established tank is probably not a sensible use of the products.
f) macroalgae fuge:
linkQ3f
No statistical difference in overall diversity in systems with/without fuges. Some major groups are affected, though. Flavobacteraceae are known from literature to be algal-surface associated, and they are measured to be higher in many tanks with macroalgae. Alteromonadaceae feed on carbohydrates, which are released by macroalgae, so in principle ought to be higher in systems with macroalgae (no mention if measured data supports that).
g) mixed reef vs SPS:
Don’t know if one is more diverse than another. No data.
h) barebottom vs sandbed
linkQ3h
No statistical difference found, but Eli believes that there wasn’t enough data and with more sandbed data - tanks with sandbeds will show more diversity than barebottom. There is a different microenvironment in the sand, so communities ought to be different. Sand has types of microbes not present in the water and/but… the diversity of aquarium sand itself is often kind of low - because sand contains big biofilms that are basically just one type.
i) skimmer?
linkQ3i
Tanks with skimmers still record good levels of pelagibacteraceae ( the most common bacteria in the water on real reefs), so it is not dangerously efficient at removing typical bacteria. Unlike UV, which can be dangerously efficient.
linkQ3i2
Hard to answer definitive statistical differences with/without skimmer, because the database of people with no skimming is so small.
j) UV ?
linkQ3j
UV strongly removes the single family common to tanks that is the most prevalent on real reefs - pelagibacteraceae. The effect is so strong that Eli can tell if your UV bulb needs replacing by whether you are running UV and still have this family. For that reason Eli likes to caution against running UV for no reason. But he always mentions that there are plenty of healthy coral tanks with UV, so it’s not an absolute need to have this group.
k) Trace elements?
LinkQ3k
Don’t know. No data on it, but the expectation from literature is that Iron certainly will. Other minor components of seawater may also.
Q4 if corals are having issues, should you check the bacteria?
LinkQ4
1st, check chemistry parameters yourself. 2nd, check ICP. 3rd then look at bacteria if no answers from the others. .
Q5 Do established tanks that are tested repeatedly show stable consistent results, or constant changes?
linkQ5
They will often test very stable month after month, and then something (a disturbance) changes and the microbiome will be totally different. These might represent nutrient shifts.
Q6 Have you tested ____ bacterial product, will you write an article?
LinkQ6
They’ve tested a bunch of products. Probably not going to be an article. He decided that making a bunch of companies mad was not a great business strategy to start with. But he is happy to run tests on products for any hobbyist who wants to know and share - he’s just not going to write an article listing the bacterial ingredients in all the hobby products.
Q7 Are some bacteria only in water, and others only on surfaces?
LinkQ7
Although some groups grow on surfaces, they are easily measured in the water. Likewise groups that live in the water are measured on surfaces. These distinctions aren’t absolutes, and the same applies to nitrifiers.
Q8 What coral pathogens are detected in the hobby?
LinkQ8
Of nine suspected pathogens responsible for Stony Coral Tissue Loss Disease, four are found in the hobby, with a couple of them in 20% of tanks. (the strongest candidate - in 100% of wild diseased corals, was in 3% of hobby tanks.) It’s impossible to know if these pathogens affect our corals because we are mixing pathogens from the caribbean with corals that aren’t from the caribbean. So they would never meet in nature, thus there’s no data on them.
There’s also an R2R thread on aquabiomics nailing down Brown Jelly Disease to one particular bacteria.
Q9 how does diversity trend over time?
LinkQ9
Tanks over time (years) tend to trend down in bacterial diversity. Avoiding this - if that’s your goal, is probably easiest done by supplementation with small occasional amounts of live sand/mud. (Be aware some bags of these products test positive for fish/coral pathogens - so it’s not an activity with no downside.)
Q10 Tank start with ammonia or ghost feeding?
LinkQ10
Ghost feeding is what Eli does. Because the community of organisms that exists on reefs and in reef tanks is large and diverse and slow to establish. Ammonia-only delays that, compared to starting with a natural food so that the rest of the community can begin maturing at the same time as the nitrifiers.
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. Corals are bombarded with bacteria on real reefs and the majority of these are pelagibacteraceae.
Q12 what group of bacteria are most closely associated with coral?
LinkQ12
Vibrio, are a group that is often thought of as concerning because it’s got many known pathogens in it, but it’s also the group that is most associated with animal surfaces like coral flesh. Coral farms can have over 50% vibrionaceae in their water samples. That doesn’t mean they have pathogens, it just means there are a lot of good and bad bacteria in that same family.
Q13 Under what situations does Eli think that live rubble and live sand/mud are useful for the bacterial community?
LinkQ13
Eli has done experiments using live reef rubble (live rock in the form of dead coral skeletons) to establish a good community to start a tank and live sand/mud to enhance a community in an established tank. Perhaps the added surface area of sand/mud makes it more useful in a system already established. But it may be that both materials are good in both situations, but the experiments are as listed above.
Q14 Do corals eat bacteria?
LinkQ14
It’s contentious among coral scientists, but there’s good evidence from radio-labeling that coral ingest nutrients from bacteria, but we have no idea what bacteria they eat. By number they encounter pelagibacteriaceae the most - but no data to say that's what they eat.
[edit: maybe links work now]
Last edited:
