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

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MnFish1

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Got my @AquaBiomics results back last week for 3 tanks.
All 3 tanks are doing quite well (images are in my sig); tests were done primarily out of curiosity.


Tank 1: ForeReefWall, 2 years 7 months, 100 g, mixed reef, live & dry rock, algae refugium, no carbon dosing, intermittent ozone use, no uv.

230 types, 0.62 diversity, 0.24 balance.

So this tank has good diversity, but it's quite different than the given distribution for the 'average' tank.
In particular, there is a high proportion of vibrionaceae and decreased pelagiobacteriaceae and flavobacteriaceae.
First, is the 'average' tank data valid? Were enough healthy reefs sampled to represent the spectrum of successful tanks?
Second, assuming my tank is off from some projected optimum ratios, what's the significance of this? In particular, the tank has virtually no pelagiobacteriaceae while others have quite a lot; is this important?

Cyanobacteria slightly elevated. However there is no cyano visible on the sand or rocks. It's possible there was some on the return nozzle at the time the sample was taken, and this would have been blown to the water sampling location. Otherwise it's hard to explain.

One fish pathogen was present! Photobacterium damselae. Looked it up, it's in the vibrio group and a fairly nasty actor. Causes outbreaks in commercial fisheries. Hemorrhagic ulcerations and sores. It's interesting because I have no sick fish currently, have never had any fish with red sores, and no fish deaths in this tank in almost 2 years. There are apparently different strains of this bacterium, and the most virulent ones contain a specific plasmid coding for toxins. It's possible that the strain or strains in my tank don't have this plasmid.

Can also infect humans who come in contact with water/fish, causes necrotizing fascitis sometimes requiring amputation and even several fatalities! Wow. Guess I should start using gloves.


Tank 2: BackReefArches, 1 year 9 months, 100 g, mixed reef, dry rock, algae refugium, no carbon dosing, intermittent ozone use, no uv.

134 types, 0.15 diversity, 0.41 balance.

This tank has low diversity, but is closer to the average tank data as far as balance.
The low diversity surprised me a bit, as the tank is thriving with a large population of fish, corals and anemones.
But on the other hand, it was started with all dry rock, so this may have been a factor.
Interestingly, even though the balance is better, this tank also has virtually no pelagiobacteriaceae. Significance?

No cyano, fish pathogens or coral pathogens.


Tank 3: NanoReefGarden, 5 months, 20 g, zoas & acans, dry rock, no refugium, no carbon dosing, no ozone or uv.

184 types, 0.38 diversity, 0.24 balance.

This tank has reasonable diversity, surprising considering how new it is, but again, not very similar to the reference data.
Again missing the pelagiobactericeae and flavobacteriaceae.
The tank has a very large proportion of methylophilaceae. No idea why or if it's significant.

No cyano, fish pathogens or coral pathogens.


So, all in all, the results were a bit surprising to me. I would have expected more diversity in the two larger older tanks. And I'm not at all clear on why certain bacterial families are virtually missing while others are in excess. Also not clear what can be done about it, or even if taking any specific action is worthwhile, likely to succeed, or make any difference. Anecdotal evidence suggests that bottled bacterial supplements are unlikely to increase diversity much. Adding pieces of live rock would probably be more beneficial, but this comes with the not insignificant risk of introducing pests which might have far more disastrous consequences than bacterial imbalance would.

Interesting data but we've still barely gotten started on what all this means.

I've already ordered some more kits; will test again in perhaps 3 months, whether I take any specific action or not.
This is interesting and more along the lines of what I would expect - ie that diversity decreases with time - rather than increases
 
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Flippers4pups

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This is interesting and more along the lines of what I would expect - ie that diversity decreases with time - rather than increases
It does it seems. Did with my tank.
 

Reesj

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Got my @AquaBiomics results back last week for 3 tanks.
All 3 tanks are doing quite well (images are in my sig); tests were done primarily out of curiosity.


Tank 1: ForeReefWall, 2 years 7 months, 100 g, mixed reef, live & dry rock, algae refugium, no carbon dosing, intermittent ozone use, no uv.

230 types, 0.62 diversity, 0.24 balance.

So this tank has good diversity, but it's quite different than the given distribution for the 'average' tank.
In particular, there is a high proportion of vibrionaceae and decreased pelagiobacteriaceae and flavobacteriaceae.
First, is the 'average' tank data valid? Were enough healthy reefs sampled to represent the spectrum of successful tanks?
Second, assuming my tank is off from some projected optimum ratios, what's the significance of this? In particular, the tank has virtually no pelagiobacteriaceae while others have quite a lot; is this important?

Cyanobacteria slightly elevated. However there is no cyano visible on the sand or rocks. It's possible there was some on the return nozzle at the time the sample was taken, and this would have been blown to the water sampling location. Otherwise it's hard to explain.

One fish pathogen was present! Photobacterium damselae. Looked it up, it's in the vibrio group and a fairly nasty actor. Causes outbreaks in commercial fisheries. Hemorrhagic ulcerations and sores. It's interesting because I have no sick fish currently, have never had any fish with red sores, and no fish deaths in this tank in almost 2 years. There are apparently different strains of this bacterium, and the most virulent ones contain a specific plasmid coding for toxins. It's possible that the strain or strains in my tank don't have this plasmid.

Can also infect humans who come in contact with water/fish, causes necrotizing fascitis sometimes requiring amputation and even several fatalities! Wow. Guess I should start using gloves.


Tank 2: BackReefArches, 1 year 9 months, 100 g, mixed reef, dry rock, algae refugium, no carbon dosing, intermittent ozone use, no uv.

134 types, 0.15 diversity, 0.41 balance.

This tank has low diversity, but is closer to the average tank data as far as balance.
The low diversity surprised me a bit, as the tank is thriving with a large population of fish, corals and anemones.
But on the other hand, it was started with all dry rock, so this may have been a factor.
Interestingly, even though the balance is better, this tank also has virtually no pelagiobacteriaceae. Significance?

No cyano, fish pathogens or coral pathogens.


Tank 3: NanoReefGarden, 5 months, 20 g, zoas & acans, dry rock, no refugium, no carbon dosing, no ozone or uv.

184 types, 0.38 diversity, 0.24 balance.

This tank has reasonable diversity, surprising considering how new it is, but again, not very similar to the reference data.
Again missing the pelagiobactericeae and flavobacteriaceae.
The tank has a very large proportion of methylophilaceae. No idea why or if it's significant.

No cyano, fish pathogens or coral pathogens.


So, all in all, the results were a bit surprising to me. I would have expected more diversity in the two larger older tanks. And I'm not at all clear on why certain bacterial families are virtually missing while others are in excess. Also not clear what can be done about it, or even if taking any specific action is worthwhile, likely to succeed, or make any difference. Anecdotal evidence suggests that bottled bacterial supplements are unlikely to increase diversity much. Adding pieces of live rock would probably be more beneficial, but this comes with the not insignificant risk of introducing pests which might have far more disastrous consequences than bacterial imbalance would.

Interesting data but we've still barely gotten started on what all this means.

I've already ordered some more kits; will test again in perhaps 3 months, whether I take any specific action or not.
Thanks for posting the results with tank details. Would really love if you can post the original result of the composition of bacteria part. We would be able to guess soem ideas and coem to some hypothsis with few more sets of these kidns of data :).

With the way things going would be amazing if we can have a look at @Paul B Tank data. Way he keeps the tank and with its age this would like the ultimate test to check how things aspire in a natural reef tank with old age.
 

lexinverts

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Thanks for posting the results with tank details. Would really love if you can post the original result of the composition of bacteria part. We would be able to guess soem ideas and coem to some hypothsis with few more sets of these kidns of data :).

With the way things going would be amazing if we can have a look at @Paul B Tank data. Way he keeps the tank and with its age this would like the ultimate test to check how things aspire in a natural reef tank with old age.
@Paul B posted his data here:
 

Reesj

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@Paul B posted his data here:
Thanks. I was away for 3-4 days and seemed missed quite a bit. It seems what I suspect is true so far from way of his tank data. With age in a stable system about 2 microbial types start to dominate a tanks. If you you started off with good diversity it would not completely go away but the composition of diffrent types seems to dwindle to smaller amounts. In short It from data so far,
If you have a health old stable reef,
You Will have a Good amount of Microbial types.( but not a lot as a starting stage tank)
You SHOULD have a low diversity score as more stable dominant strain or 2 take over the tank.
 
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Flippers4pups

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Thanks. I was away for 3-4 days and seemed missed quite a bit. It seems what I suspect is true so far from way of his tank data. With age in a stable system about 2 microbial types start to dominate a tanks. If you you started off with good diversity it would not completely go away but the composition of diffrent types seems to dwindle to smaller amounts. In short It from data so far,
If you have a health old stable reef,
You Will have a Good amount of Microbial types.( but not a lot as a starting stage tank)
You SHOULD have a low diversity score as more stable dominant strain or 2 take over the tank.
Thus adding some diversity from live rock directly from the ocean. Could kick start the other strains.

The question is why. The ocean must supply these in abundance constantly, where in a tank what keeps these going is missing. What keeps them healthy and abundant? That's the question.
 

MnFish1

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Thus adding some diversity from live rock directly from the ocean. Could kick start the other strains.

The question is why. The ocean must supply these in abundance constantly, where in a tank what keeps these going is missing. What keeps them healthy and abundant? That's the question.
Yes its interesting - I think certain bacteria out-compete other bacteria in tanks much like the following scenario - put a lion a tiger a mouse and an elephant in a room - eventually only 1 or 2 animals will remain - depending on food. The diversity at the start - in a closed system - will usually decrease with time.

There is very little evidence (that I have seen) - that adding 'more' species will increase diversity
 

AquaBiomics

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One fish pathogen was present! Photobacterium damselae. Looked it up, it's in the vibrio group and a fairly nasty actor. Causes outbreaks in commercial fisheries. Hemorrhagic ulcerations and sores. It's interesting because I have no sick fish currently, have never had any fish with red sores, and no fish deaths in this tank in almost 2 years. There are apparently different strains of this bacterium, and the most virulent ones contain a specific plasmid coding for toxins. It's possible that the strain or strains in my tank don't have this plasmid.

Can also infect humans who come in contact with water/fish, causes necrotizing fascitis sometimes requiring amputation and even several fatalities! Wow. Guess I should start using gloves.
Hi Randy,

Thanks for posting this detailed description. So many interesting things to explore here.

First I want to mention the pathogen. As you describe, there are lots of different types of P. damselae (including 2 subspecies with multiple strains), many of which are really nasty for a broad range of fish. It's so-named for its occurrence in the Damsel family, but the range is so broad I hesitate to say which aquarium fish it infects. I believe there are some fish disease experts on the forum though, maybe @Humblefish has some thoughts on this bug? It causes diseases called Photobacteriosis or pasteurellosis, which are widely described in the aquaculture literature but I can find little information on saltwater aquarium fish.

A few details I can contribute -
  • This exact same bug is found in about 1 out of 8 tanks. None of mine have it so I cannot comment on effects or lack thereof. But several others have reported no symptoms in their fish. It might be interesting to compare fish lists, especially if we can find out what it infects outside of the Damsel family.
  • At the DNA sequence level, this marker cannot distinguish between different strains, since it is a perfect match to multiple strains both the piscidida and damselae subspecies. I want to emphasize this point -- the data in hand can't distinguish between strains that are pathogenic for fish, humans, both, or neither.
  • Some researchers consider this group some of the most dangerous pathogens in global aquaculture (source), because it is globally distributed, infects a broad range of fish, and has a high mortality rate upon infection.
I didnt know which if any bacterial fish pathogens to expect in a broad survey of aquariums. So I searched for all the names I could find in the literature (over 40). This bug is the only known fish pathogen I've seen, and it shows up repeatedly but not universally (about 1 out of 8 tanks). Considering the range of possible effects I think its worth paying attention to, but I don't want to either falsely alarm or reassure anyone.

While we're on the subject of zoonoses in aquariums, I always search for Mycobacterium marinum and am happy to report I have not found it yet. I've known someone infected by M. marinum (it causes Aquarium granuloma) so while it's rare its far from unheard of.

I will say, I'm the farthest thing from a germ phobe and have accidentally gargled my share of tank water while siphoning. But after spending so much time looking at aquarium microbiomes this year I am paying special attention to keep any open cuts out of the water, at the very least...
 
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AquaBiomics

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Thanks. I was away for 3-4 days and seemed missed quite a bit. It seems what I suspect is true so far from way of his tank data. With age in a stable system about 2 microbial types start to dominate a tanks. If you you started off with good diversity it would not completely go away but the composition of diffrent types seems to dwindle to smaller amounts. In short It from data so far,
If you have a health old stable reef,
You Will have a Good amount of Microbial types.( but not a lot as a starting stage tank)
You SHOULD have a low diversity score as more stable dominant strain or 2 take over the tank.
I sure can't argue with the conclusion a lot of people are favoring here, that diversity decreases with time. Theres a good theoretical basis for expecting it, and the data seem to lean in that direction. I just want to caution that I have very few old tanks in the dataset, and the relationship is not statistically significant yet.
I'm recruiting a few local old tanks for my next batch to make the dataset more balanced.

I also question whether, even if diversity declines with time, is that a good thing? After all, if we're speculating based on small numbers of tanks, I'll point out that Paul B's 47 yr old tank has the diversity of the average 5 year old tank, higher than that of his nearest runners up...

Lately, anytime the subject of diversity comes up, I feel compelled to repeat my current mantra that while I don't know the ideal level of diversity, since we don't know so many of the microbial functions, I consider diversity to be generally positive as a strategy for collecting the types that turn out to have beneficial functions.

Kind of long, for a mantra, I should work on that.
 

AquaBiomics

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In particular, the tank has virtually no pelagiobacteriaceae while others have quite a lot; is this important?
I also want to address this, then I'll stop spamming for a bit.

One of the questions people often ask me is how our tanks microbiomes compare to the ocean, and I have to say they are quite different. As I think we're all starting to see, many of them are even very different from each other (although they also have a lot in common; see this description of the first 20 tanks I surveyed).

But speaking in terms of numbers, the biggest thing they have in common is this - Pelagibacteraceae. Many of you may be familiar with the name SAR11, an earlier descrition for this group. This is the most abundant group of bacteria in most parts of the ocean (source). If we want our tanks' microbiomes to look like the ocean, this is a big part of what we want.

My tanks are also low in Pelagibacteraceae, so I am interested to explore this question further even if only for my own selfish interests. I can't say whether this group is needed, but can say for sure that if we don't have them, thats a notable difference between our tanks and the natural environment.

This group is specialized for a low dissolved nutrient environment (like the open ocean or the coral reef), but I don't see any clear relationship with NO3 or PO4 so far. They have specific nutritional requirements that suggest avenues for experiments...

e.g. these require DOC and I don't do any carbon dosing, while many people with higher Pelagibacteraceae do... are you dosing carbon at all? (I looked at your log but am not clear on whether Fuel is used as a carbon source or primarily for the other micronutrients)
 

Scott Campbell

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I also want to address this, then I'll stop spamming for a bit.

One of the questions people often ask me is how our tanks microbiomes compare to the ocean, and I have to say they are quite different. As I think we're all starting to see, many of them are even very different from each other (although they also have a lot in common; see this description of the first 20 tanks I surveyed).

But speaking in terms of numbers, the biggest thing they have in common is this - Pelagibacteraceae. Many of you may be familiar with the name SAR11, an earlier descrition for this group. This is the most abundant group of bacteria in most parts of the ocean (source). If we want our tanks' microbiomes to look like the ocean, this is a big part of what we want.

My tanks are also low in Pelagibacteraceae, so I am interested to explore this question further even if only for my own selfish interests. I can't say whether this group is needed, but can say for sure that if we don't have them, thats a notable difference between our tanks and the natural environment.

This group is specialized for a low dissolved nutrient environment (like the open ocean or the coral reef), but I don't see any clear relationship with NO3 or PO4 so far. They have specific nutritional requirements that suggest avenues for experiments...

e.g. these require DOC and I don't do any carbon dosing, while many people with higher Pelagibacteraceae do... are you dosing carbon at all? (I looked at your log but am not clear on whether Fuel is used as a carbon source or primarily for the other micronutrients)
With regard to a free swimming bacterial strain like Pelagibacteraceae, is it possible older tanks with a higher density of filter feeders like corals, sponges, tunicates, etc. simply consume the bacteria as fast as they reproduce? Perhaps like hair algae in a tank with a lot of herbivores, consumers keep the population densities low despite the conditions being optimal for growth. So that what shows up in a test like this are simply the bacterial strains that are not readily consumed. Like the wiry turf algae in my tank no one seems to eat. The test might not reflect the overall health or viability of a strain of bacteria. It may not be that Rhodobacteraceae are stomping Pelagibacteraceae out of existence in my tank. My corals may simply not readily feed on Rhodobacteraceae. Which is certainly an advantage for the Rhodobacteraceae - but not necessarily an indication the bacterial "balance" or bacterial "health" of the tank is askew.

What makes me think this is plausible are the extremely low numbers for the nitrogen processing bacterial strains in many tanks. Clearly these bacteria are present and are generating nitrate (at least in my tank). But their numbers might be low because they are competing for ammonia with a dense population of corals in a closed system. Remove the competition and/or predators and perhaps the nitrogen processing bacteria and bacteria like Pelagibacteraceae return to more "normal" or "typical" levels.

I think what is interesting about the results from Paul B's tank is that he has successfully maintained good diversity by regularly replenishing bacteria with NSW, mud, fresh oysters as food, etc. So most bacterial strains are always present. But even with Paul's tank Pelagibacteraceae numbers are lower than expected and there is (as with other tanks) some outlier bacterial strain that exists in unexpectedly large numbers. I'm wondering if the corals and sponges in Paul's tank are shaping these numbers based on what they primarily feed on. So that more "typical" tanks are not over-consuming or over-harvesting certain bacterial strains while "atypical" tanks (like mine and Paul's) have matured to a point at which coral growth might be limited by specific bacterial food sources.

Which leads me to another issue about my tank that has always puzzled me. I have one green plating montipora that always dies back as fast as it grows. It seems as if my tank can only support a fixed volume of this coral. If I trim it back, it dies back less. As it dies back, it immediately starts to re-grow - often growing right back over the dead areas. It never dies back much and does not seem like any kind of RTN. I have assumed there was some limiting trace element but after 4+ years of ICP tests my tank does not seem limited in such a manner. Now I am wondering if the coral is simply using up a critical bacterial food source and starving - causing it to die back to a point where there is sufficient food.

I am sure there are bacterial strains and bacterial proportions that will be found to be less than ideal for our tanks. But I am wondering if "typical" tanks are mostly just tanks that are not yet hitting up against the wall of available food sources (so that bacterial proportions are still relatively similar to natural ocean levels) while "atypical" tanks have matured in such a way that coral and sponge growth are shaping and altering the perceived bacterial population densities through consumption. Both types of tanks might be equally healthy and viable. They would just test very differently.

Just my thoughts. Hard for me to not spend my days thinking about all this. :)
 

AquaBiomics

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With regard to a free swimming bacterial strain like Pelagibacteraceae, is it possible older tanks with a higher density of filter feeders like corals, sponges, tunicates, etc. simply consume the bacteria as fast as they reproduce? Perhaps like hair algae in a tank with a lot of herbivores, consumers keep the population densities low despite the conditions being optimal for growth. So that what shows up in a test like this are simply the bacterial strains that are not readily consumed. Like the wiry turf algae in my tank no one seems to eat. The test might not reflect the overall health or viability of a strain of bacteria. It may not be that Rhodobacteraceae are stomping Pelagibacteraceae out of existence in my tank. My corals may simply not readily feed on Rhodobacteraceae. Which is certainly an advantage for the Rhodobacteraceae - but not necessarily an indication the bacterial "balance" or bacterial "health" of the tank is askew.

What makes me think this is plausible are the extremely low numbers for the nitrogen processing bacterial strains in many tanks. Clearly these bacteria are present and are generating nitrate (at least in my tank). But their numbers might be low because they are competing for ammonia with a dense population of corals in a closed system. Remove the competition and/or predators and perhaps the nitrogen processing bacteria and bacteria like Pelagibacteraceae return to more "normal" or "typical" levels.

I think what is interesting about the results from Paul B's tank is that he has successfully maintained good diversity by regularly replenishing bacteria with NSW, mud, fresh oysters as food, etc. So most bacterial strains are always present. But even with Paul's tank Pelagibacteraceae numbers are lower than expected and there is (as with other tanks) some outlier bacterial strain that exists in unexpectedly large numbers. I'm wondering if the corals and sponges in Paul's tank are shaping these numbers based on what they primarily feed on. So that more "typical" tanks are not over-consuming or over-harvesting certain bacterial strains while "atypical" tanks (like mine and Paul's) have matured to a point at which coral growth might be limited by specific bacterial food sources.

Which leads me to another issue about my tank that has always puzzled me. I have one green plating montipora that always dies back as fast as it grows. It seems as if my tank can only support a fixed volume of this coral. If I trim it back, it dies back less. As it dies back, it immediately starts to re-grow - often growing right back over the dead areas. It never dies back much and does not seem like any kind of RTN. I have assumed there was some limiting trace element but after 4+ years of ICP tests my tank does not seem limited in such a manner. Now I am wondering if the coral is simply using up a critical bacterial food source and starving - causing it to die back to a point where there is sufficient food.

I am sure there are bacterial strains and bacterial proportions that will be found to be less than ideal for our tanks. But I am wondering if "typical" tanks are mostly just tanks that are not yet hitting up against the wall of available food sources (so that bacterial proportions are still relatively similar to natural ocean levels) while "atypical" tanks have matured in such a way that coral and sponge growth are shaping and altering the perceived bacterial population densities through consumption. Both types of tanks might be equally healthy and viable. They would just test very differently.

Just my thoughts. Hard for me to not spend my days thinking about all this. :)
I've been thinking about similar things - competition between animals, algae, and microbes for nutrients.

Many of us start with this idea that all the ammonia gets converted to nitrite by some microbes, then converted to nitrate by others, and perhaps eventually to N2 gas by others. As if those were the only processes that consume NH3, NO2, or NO3... in fact, we know that algae (among other things) will also take up these nutrients and convert them to biomass rather than spitting them back out as NO2 or NO3.

Symbiotic animals like the corals in all our tanks and that big sponge in Paul's also take them up to feed their symbionts, again without necessarily converting them and spitting them back out...

One of the biggest surprises coming out of this is the variation in nitrite oxidizing bacteria among tanks. Some tanks have plenty of these, so its not like we can't detect them. I am coming to think that some of our tanks are actually processing more ammonia through algae and animals, while others are processing more through microbes. I sometimes hear people talk about a bacterial-dominated or algae dominated system; I think we may be seeing evidence of that here.

Before I started this, I would have predicted all established tanks had high populations of NOB. Now I'm not so sure. I see consistent variation among tanks. To confirm whether this is related to nitrite oxidizing activity, I'm gonna spike some of my experimental tanks with nitrite and do some measurements of nitrite depletion. More and more, I am coming to believe that in fact there are previously undiagnosed differences in the levels of nutrient processing bugs in our tanks. (Likely because other things in the tank are competing for the same nutrients)

--

On the free-living bugs, like Pelagibacteraceae. I absolutely think it makes sense that a system with more filter feeders that consume bacteria (sponges, tunicates, some gorgonians, probably some corals) would have less of the free living bugs. Since the surface associated bugs in the water column would be constantly replenished by shedding from surfaces, while bugs that lived only in the water would be preferentially depleted.

I am very attracted to this theory, my only hesitation is that skimmers should have similar effects, but my skimmerless tank has less Pelagi than my tanks with skimmers. And none of my tanks have a very impressive amount of sponges. And my tank with thriving SPS is the only one with high Pelagi.

I'm glad I'm not the only one spending time thinking about this! I think there are lots of surprises and interesting mysteries in store as we continue to gather these data.
 

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I've been thinking about similar things - competition between animals, algae, and microbes for nutrients.

Many of us start with this idea that all the ammonia gets converted to nitrite by some microbes, then converted to nitrate by others, and perhaps eventually to N2 gas by others. As if those were the only processes that consume NH3, NO2, or NO3... in fact, we know that algae (among other things) will also take up these nutrients and convert them to biomass rather than spitting them back out as NO2 or NO3.

Symbiotic animals like the corals in all our tanks and that big sponge in Paul's also take them up to feed their symbionts, again without necessarily converting them and spitting them back out...

One of the biggest surprises coming out of this is the variation in nitrite oxidizing bacteria among tanks. Some tanks have plenty of these, so its not like we can't detect them. I am coming to think that some of our tanks are actually processing more ammonia through algae and animals, while others are processing more through microbes. I sometimes hear people talk about a bacterial-dominated or algae dominated system; I think we may be seeing evidence of that here.

Before I started this, I would have predicted all established tanks had high populations of NOB. Now I'm not so sure. I see consistent variation among tanks. To confirm whether this is related to nitrite oxidizing activity, I'm gonna spike some of my experimental tanks with nitrite and do some measurements of nitrite depletion. More and more, I am coming to believe that in fact there are previously undiagnosed differences in the levels of nutrient processing bugs in our tanks. (Likely because other things in the tank are competing for the same nutrients)

--

On the free-living bugs, like Pelagibacteraceae. I absolutely think it makes sense that a system with more filter feeders that consume bacteria (sponges, tunicates, some gorgonians, probably some corals) would have less of the free living bugs. Since the surface associated bugs in the water column would be constantly replenished by shedding from surfaces, while bugs that lived only in the water would be preferentially depleted.

I am very attracted to this theory, my only hesitation is that skimmers should have similar effects, but my skimmerless tank has less Pelagi than my tanks with skimmers. And none of my tanks have a very impressive amount of sponges. And my tank with thriving SPS is the only one with high Pelagi.

I'm glad I'm not the only one spending time thinking about this! I think there are lots of surprises and interesting mysteries in store as we continue to gather these data.
Has a test been done on a skimmate sample? Might be enlightening to know what bacteria a skimmer is pulling out.
 

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is it not the case that most nitrifying bacteria are in the substrate and rockwork, so unless the mats are disturbed prior to the test sample being taken that these levels would be lower?
 
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e.g. these require DOC and I don't do any carbon dosing, while many people with higher Pelagibacteraceae do... are you dosing carbon at all? (I looked at your log but am not clear on whether Fuel is used as a carbon source or primarily for the other micronutrients)
Thanks for the reply. Yes I did focus on the pelagiobacteriaceae specifically because of how prevalent they are in open ocean waters, and yet not in my tanks or many other tanks.

I do not carbon dose. (I only use small quantities of Fuel, not carbon-dosing quantities.) I've had negative experiences in the past with it which I don't need to get into, but I'm cautious about starting it again. On a general theoretical level, increasing the bacterial concentration in tank water to high levels (which is what carbon dosing does) just seems like a bad idea to me as far as oxygen levels, as well as the potential for pathogens harming fish, corals, snail or crustaceans. Although I certainly acknowledge that many use carbon dosing successfully without adverse effect.

I'll say this - The algae in my fuge doesn't like it much when I carbon dose.

Can you expand a bit on those who carbon dose having a higher bacterial diversity and more pelagiobacteria?
Is it a significant and consistent difference? Does it represent a potential reason to begin carbon dosing?
 

rkpetersen

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This group is specialized for a low dissolved nutrient environment (like the open ocean or the coral reef), but I don't see any clear relationship with NO3 or PO4 so far. They have specific nutritional requirements that suggest avenues for experiments...
Thanks, I'd looked at that table when I sent the samples in but didn't remember this. So they require glycine and DOC?
That's very interesting! And interesting that glycine is not one of the amino acids in Fuel.
I wonder which of the available amino acid supplements contain glycine specifically?
Fuel is the only one I have at the moment, and I don't see specific ingredients for other products online.
Lots of folks swear by AcroPower; perhaps it contains glycine? And what about Reef Energy?

It would be interesting to see if carbon dosing with the addition of glycine supplement increases pelagiobacteria.

Another way of addressing this question is this -
Based on your data, what supplement products are those with sizable pelagiobacteria concentrations using?
 

Mortie31

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But speaking in terms of numbers, the biggest thing they have in common is this - Pelagibacteraceae. Many of you may be familiar with the name SAR11, an earlier descrition for this group. This is the most abundant group of bacteria in most parts of the ocean (source). If we want our tanks' microbiomes to look like the ocean, this is a big part of what we want.
They may be commonplace but do we know what they do, and there importance to the reef zones? and are they necessary enough for there low levels in our tanks to be of initial concern?
 

AquaBiomics

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is it not the case that most nitrifying bacteria are in the substrate and rockwork, so unless the mats are disturbed prior to the test sample being taken that these levels would be lower?
Good question, you are correct that most but not all nitrifying microbes are surface associated. They are more abundant in biofilm samples than water samples.

While some of my earlier reports were based on water samples alone, all the client results being discussed in this thread include both water and biofilm samples.
 

MnFish1

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is it not the case that most nitrifying bacteria are in the substrate and rockwork, so unless the mats are disturbed prior to the test sample being taken that these levels would be lower?
Most nitrifying bacteria are 'motile' - they can go to wherever the food source is the greatest. It was once thought that they just sat in one place - that is not the case. More interesting is that there are many more bacteria that are nitrifying than the ones we commonly 'desire'
 
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