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

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Mortie31

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After seeing the recent results posted (thanks all for sharing) a couple of questions spring to mind.
1) How typical is the “typical” reference system results? Are they from an average of tanks of varying age, coral types, started dead rock/ bac, started with live Indo or Caribbean rock?
2) As far as I understand it various corals/ algae will consume different molecules preferentially depending on levels available, some NH4, NH3, NO3 (forgive me if I’m wrong on those) so would this shift the microbe balance As levels they consume may vary?
3) How would a biome balance shift depending on the levels of fish waste produced in a tank? one of the results recently published was from a low fish load high algae tank, to me that may cause a shift from nitrifying bacteria to other types.. purely on what food sources are available, I could be totally wrong as I’ve had to simplify it in my mind...
 

Reesj

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Thanks for posting the results. If more people can post their results, it would be amazing with a small bit about their tank setup and age. Will really help people in this forum to further their knowledge.
 

Nano sapiens

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Another question of interest that I have is when new species of bacteria are added to an older system that has an established and fully functional (yet much reduced) microbiome, how effective would the new bacteria be in establishing themselves? Basically, would the new comers be able to make significant headway and at least partial displace the entrenched ones, or would they be relegated to the sidelines awaiting some major system disturbance in order to proliferate? This is where 'before and after' testing would be crucial to answering such basic, yet important, questions.
 

taricha

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For those who are concerned about their bacterial diversity, I've seen suggestions of bottled bacteria a few times.
But look at the posted results. If you are deep in the red, in very low diversity, you could still have 100 sequences. How many do you think come out of a bottled bacteria product? One? 5 to 10 if it's a "bacterial blend"?
I can't see that shifting the score much.
But an actual piece of live rock from the ocean, that would give you the chance to add hundreds possibly.
[Leaving aside the question of whether the bacterial diversity number / score is worth chasing.]
 

taricha

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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.
What do we make of this? I'm not even coming up with good conjectures here.
Lots of hungry mouths for ammonia, barely any for nitrite. Where's the missing parts of the nitrogen cycle?
 
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AquaBiomics

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For those who are concerned about their bacterial diversity, I've seen suggestions of bottled bacteria a few times.
But look at the posted results. If you are deep in the red, in very low diversity, you could still have 100 sequences. How many do you think come out of a bottled bacteria product? One? 5 to 10 if it's a "bacterial blend"?
I can't see that shifting the score much.
But an actual piece of live rock from the ocean, that would give you the chance to add hundreds possibly.
[Leaving aside the question of whether the bacterial diversity number / score is worth chasing.]
I agree with this reasoning completely.

To be clear, I'm not anti-bottled bacteria per se. As many hobbyists have found, they are effective in rapidly processing wastes in a new tank. But I've done an experiment with one of the widely used products, and it didnt seem to have much effect at all on the community. I'll post that article as soon as my live rock one gets approved and discussed :)

I think the use of bottled bacteria to enhance microbial diversity - which appears to be an "off-label" application for most of these products - is a practice with little evidence to support it.

Live rock, as fresh from the ocean as possible... this rapidly enhances diversity in a new tank, and produces a community similar to an established tank within a week or two. Generally, if I was looking to introduce new microbes, I'd get some good live rock.
 

AquaBiomics

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After seeing the recent results posted (thanks all for sharing) a couple of questions spring to mind.
1) How typical is the “typical” reference system results? Are they from an average of tanks of varying age, coral types, started dead rock/ bac, started with live Indo or Caribbean rock?
2) As far as I understand it various corals/ algae will consume different molecules preferentially depending on levels available, some NH4, NH3, NO3 (forgive me if I’m wrong on those) so would this shift the microbe balance As levels they consume may vary?
3) How would a biome balance shift depending on the levels of fish waste produced in a tank? one of the results recently published was from a low fish load high algae tank, to me that may cause a shift from nitrifying bacteria to other types.. purely on what food sources are available, I could be totally wrong as I’ve had to simplify it in my mind...
You raise important questions!

1. Its simply the average across all "real hobbyist tanks" that I've surveyed. I didnt include experimental tanks, or my own home tanks... its intended to be an open survey of hobbyist tanks that at this point includes about 30-40 tanks. The details you ask about are interesting. I'll compile those and add a statement in the FAQ about it. It would be nice to have a constantly updated description of what's included in the database of tanks used to find the "typical" levels.
There was a lot of variation among tanks e.g. age, live vs dry rock, etc.

2. There is certainly competition among everything in the tank for dissolved nutrients. Each living thing has nutrients it likes and others it doesnt, and each has its own capacity to take them up. In this complex tug of war over nutrients, I think its safe to say (a) the animals and algae in the tank can affect the nutrients available, thus affecting microbial communities. and (b) we don't know enough about these interactions to make any really clear predictions yet (like "animal X promotes microbe Y").

I think the really interesting area to explore here will be DOC, which is a hugely complex mixture and the type of DOC appears to have a big effect on microbial communities in the ocean.

3. I agree, bioload seems like an important factor here. Most of the DON probably comes from fish waste in our systems, so the number of fish is likely to affect the community. I should add this to the sample survey... I wonder how to capture this. Total system volume and total number of fish-inches? What do you think?
 

Mortie31

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I think the really interesting area to explore here will be DOC
Triton are offering N-DOC testing, but that has been met with a lot of scepticism and there explanation of how there guidance was arrived at divides a lot of reefers.. but several people have used it an ethereal are threads in here if your not familiar with it, maybe someone has used both your microbiome and N-doc testing.
I agree, bioload seems like an important factor here. Most of the DON probably comes from fish waste in our systems, so the number of fish is likely to affect the community. I should add this to the sample survey... I wonder how to capture this. Total system volume and total number of fish-inches? What do you think?
IMO there are so many variables for me a starting point would be
volume
Age
live or dead rock and bottled bac
SPS, mixed or FO
Fish Inches is a good one (but efficiency of filtration will affect this widely)
Maybe NO3 and PO4 levels would give a better guesstimate load
 

Randy Holmes-Farley

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[QUOTE="AquaBiomics, post: 6758901, member: 132350”] 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.
[/QUOTE]

Ever since folks started dosing organic carbon, there had been this hypothesis that diversity is better (with the corollary that dosing one type of carbon leads to less diversity).

I have long challenged the basis for these assertions. I don't see any science behind them. Maybe long term it may become available, but I don’t think it is established today.

That said, I have done things to establish diversity (like water changes with fresh NSW), but didn’t notice any apparent effects.
 

AquaBiomics

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Ever since folks started dosing organic carbon, there had been this hypothesis that diversity is better (with the corollary that dosing one type of carbon leads to less diversity).

I have long challenged the basis for these assertions. I don't see any science behind them. Maybe long term it may become available, but I don’t think it is established today.

That said, I have done things to establish diversity (like water changes with fresh NSW), but didn’t notice any apparent effects.
I agree - while Ecologists have long appreciatedthe general benefits of diversity in natural ecosystems including ecosystem services, productivity, and stability, this doesnt mean "more diversity is always better" in a specific case.

The question is, in a specific ecosystem with a given level of diversity, what happens if we increase or decrease that diversity? And I emphatically agree that for home aquariums we do not know the answer to this. Specifically,
1. What is the relationship between microbial diversity and aquarium ecosystem health? What is the shape of this function... Is more always better? Is there an optimum intermediate level? Is there a saturating relationship where enough is enough, and more doesnt help?
2. What are the ideal levels themselves (i.e., if its a saturating relationship, what is the point of diminishing returns?)

This is why I started by describing the range of diversity among tanks, and why I express the results in terms of percentiles. I don't think anyone can say with confidence whether (for example) 150 types is the ideal diversity. What we can say with some confidence is that 70% of tanks surveyed have higher diversity than this.

I also have data supporting the idea that diversity isnt the only thing that matters. My experimental tanks started with low-quality live rock have relatively high diversity, but an imbalanced community (i.e. the abundance of each family in these tanks was poorly correlated with their levels in typical reef tanks). These tanks had weaker nitrification and much more nuisance algae (the uglies) than the tanks with high quality live rock (high diversity, balanced communities). These should show up as soon as my article gets converted from a post to an article. Any day, I hope!

Ultimately, ecosystem functions depend not just on how many types are there, but on what they do. Lacking detailed knowledge of each microbial types' activities, we use diversity as a very imperfect guide to collecting enough of the types that matter.

But I think it is only one of the metrics to look at, and just like different reef keepers swear by different levels of dKH or Mg, I imagine there will be different schools of thought with regard to diversity too.
 

AquaBiomics

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@AquaBiomics what effect does dark vs light (i.e. time of day) have on your results?
Its a good question, time of day affects so many things in our tanks, including water chemistry, that it seems almost inevitable it would have some effect on the microbial community. Of course, the time scale of microbial reproduction relative to the light cycle is likely to dampen this effect... fast-growing types could e.g. bloom during the day but many marine microbes have longer doubling times.

I don't have data yet but plan a short time series in the next round to address both this point and the more general question of short term stability in the microbiome of an established tank.
 

MnFish1

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Its a good question, time of day affects so many things in our tanks, including water chemistry, that it seems almost inevitable it would have some effect on the microbial community. Of course, the time scale of microbial reproduction relative to the light cycle is likely to dampen this effect... fast-growing types could e.g. bloom during the day but many marine microbes have longer doubling times.

I don't have data yet but plan a short time series in the next round to address both this point and the more general question of short term stability in the microbiome of an established tank.
Thanks the question was partly based on the fact the (IF) time of day makes a difference - would it be an idea to check samples at a certain time - otherwise if one person does it at 8AM and 1 at 10PM etc etc - How would one know if the 'diversity' seen relates to the conditions when the sample was taken - as compared to the 'control tanks'

Also thought of a different question - aside from seeing if varying coral pathogens are present (which is great) - could time of day affect their numbers (i.e. more active after lights have been on etc etc). In any case - thanks for responding.
 

2una

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@AquaBiomics
Any coral problem tanks to date with cases of Vibrio raising its head very much?
Love what your doing here & tagging along with interest.
 

AquaBiomics

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Here are my results! I apparently have perhaps the most atypical tank possible with minimal diversity. Looks like one strain of bacteria accounts for roughly half the bacteria in my tank. o_O My tank is roughly 32 years old and I have never done anything to increase bacterial diversity. And the tank is completely overgrown so I rarely add anything new outside of the occasional snail or hermit crab. I do spend a lot of effort trying to maintain microfauna diversity (growing my own copepods, maintaining a refugium, growing various macroalgae, etc.) but that apparently has no significant effect on bacterial diversity.

My guess is that my tank has simply become less diverse as a function of age. I don't have any problems however. Fish are all healthy and have been with me for years. One for a couple decades. Corals grow quickly. I have a complete hodgepodge of corals that I have acquired over the years. Without some compelling reason, I can't imagine I will do anything to try to change the bacterial make-up of my tank. Not even sure how possible it is at this point to displace the mighty Rhodobacteria that rule my reef.

I plan on testing again in 6 months to see if anything changes. I will not be doing anything to try to affect a change however. This will simply be a second test to see if my diversity is staying the same or dropping further over time.

My expectation was that a high degree of bacterial diversity was probably desirable. Perhaps even critically important. Now I am not sure. My tank obviously seems fine with one dominant bacterial strain. Very interesting stuff! Excited to see other tank results!!


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Hi Scott,

Here's my perspective on your results.

Your tank's community is on the lower end of diversity. To put this in context, about half the tanks in this batch had a diversity between 144-268. So yours is right on the edge of this 'normal range'. Any lower, and I start to wonder why.

The balance of your community is very different from the typical reef tank. This can be best seen in part 2 -- you have LOTS of Rhodobacteraceae. While this is a normal part of the core aquarium microbiome, its much more abundant in your sample relative to others. You also have fairly high levels of HTCC2188, a poorly-characterized (and named) family that is not usually present at high levels. You also have very little Pelagibacteraceae or Flavobacteriaceae, which are dominant components of the typical tanks' microbiome.

I'm very interested to hear you have grown a lot of macro in your system over the years. Rhodobacteraceae are associated with algal biofilms as mentioned in this thread already, and also have some interested nutritional requirements associated with algae (they like several major algal metabolites including DMSP and methylated amines).

Overall I share your observation, its interesting that such an established tank would have low diversity. I've read compelling arguments why diversity should either increase or decrease over time, but yours is certainly a point in favor of the latter. I have not found significant effects of age on diversity yet in these data but its a question high on the list. There is a non significant trend so far toward lower diversity in older tanks...

I think I read that you're relying mostly on carbon dosing for nutrient export these days instead of algae, is that right? What carbon source are you dosing? I am very interested in tracking down associations with carbon dosing, so we can identify what are typical responses to each source.
 
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AquaBiomics

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@AquaBiomics
Any coral problem tanks to date with cases of Vibrio raising its head very much?
Love what your doing here & tagging along with interest.
Vibrionaceae continues to be one of the most variable families, which for a family full of pathogens makes it an interesting one to watch! In this batch it ranged from 0-34% of the microbiome, in different samples.
None of the Vibrios were known pathogenic types, although I'm sure there are lots of undescribed pathogens in this group and most of the Vibrios in aquariums are described members of the genus.

Without revealing any individual data I will say this - the two tanks with high Vibrio levels both have hard corals and neither of their owners reported any problems with coral disease in their tanks. So this continues to support the view that Vibrio is a normal (but not inevitable) part of the aquarium microbiome, and high levels of the family are probably not a cause for alarm.

I do continue to screen for specific Vibrio pathogens, and will be looking into the database for associations between specific Vibrio types and reported symptoms. Perhaps there are specific types (previously unknown) that are associated with symptoms... but family level abundance does not appear to be, so far.
 

Scott Campbell

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Hi Scott,

Here's my perspective on your results.

Your tank's community is on the lower end of diversity. To put this in context, about half the tanks in this batch had a diversity between 144-268. So yours is right on the edge of this 'normal range'. Any lower, and I start to wonder why.

The balance of your community is very different from the typical reef tank. This can be best seen in part 2 -- you have LOTS of Rhodobacteraceae. While this is a normal part of the core aquarium microbiome, its much more abundant in your sample relative to others. You also have fairly high levels of HTCC2188, a poorly-characterized (and named) family that is not usually present at high levels. You also have very little Pelagibacteraceae or Flavobacteriaceae, which are dominant components of the typical tanks' microbiome.

I'm very interested to hear you have grown a lot of macro in your system over the years. Rhodobacteraceae are associated with algal biofilms as mentioned in this thread already, and also have some interested nutritional requirements associated with algae (they like several major algal metabolites including DMSP and methylated amines).

Overall I share your observation, its interesting that such an established tank would have low diversity. I've read compelling arguments why diversity should either increase or decrease over time, but yours is certainly a point in favor of the latter. I have not found significant effects of age on diversity yet in these data but its a question high on the list. There is a non significant trend so far toward lower diversity in older tanks...

I think I read that you're relying mostly on carbon dosing for nutrient export these days instead of algae, is that right? What carbon source are you dosing? I am very interested in tracking down associations with carbon dosing, so we can identify what are typical responses to each source.
I still grow a lot of macroalgae but have been using carbon dosing as a way to make overall export easier and more efficient. I use a homemade mix of vodka, vinegar and sugar. Heavy on the vodka.
 

Scott Campbell

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Just out of interest what recipe do you use? I use 700ml vodka +1300ml vinegar, I don’t use sugar, do u think it adds anything?
Am away from home so this is from memory - but I think 250 ml vodka, 50 ml vinegar and 1.5 teaspoons sugar. I feel like I got the formula on this forum. A few years back though. Have no clue if the sugar is helpful. Just stuck with the original formula regardless!
 

rkpetersen

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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.
 
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