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

[Kenneth Wingerter]

was recently reading that rhizobial and nonpathogenic vibrio are incredibly important to the coral holobiont. these and other diazotrophic bacteria can be 400 times as abundant in coral mucus as in the surrounding waters. perhaps this disparity can be even greater where uv sterilization is used. question for eli... if i were to send samples from a reef tank, is there any way to directly test coral mucus samples? if so, how much mucus would be needed? thanks!

 

[MnFish1]

@AquaBiomics did you ever finish our experiment?

 

[robinhood639]

Fascinating discussion. Seems that that thread has gone dormant for a while... Did the discussion shift to another thread?

 

[taricha]

check user aquabiomics posts. Active discussions of the testing service in secveral different threads and a few articles on the board.

 

[MnFish1]

@AquaBiomics. hey - did you ever complete our experiment

 

[Nano sapiens]

A similar reef microbial study to the one I posted on page 20, but this one is from the Caribbean and examined microorganism communities on three islands:

https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0229442


Reposting the Pacific diel reef microbial study for ease or reference/comparison:

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

 

[Pygmey]

Any new info here? Seems the thread has died and it would be good to read some updates.

 

[MnFish1]

Any new info here? Seems the thread has died and it would be good to read some updates.

What info do you want?

 

[ReefBeta]

What have we learnt from testing microbes? What actions can be resulted from a test result,?

 

[MnFish1]

What have we learnt from testing microbes? What actions can be resulted from a test result,?

That is for @AquaBiomics to answer. I'm not sure there is an answer after reading multiple threads about this. One benefit of testing - is to see if you have pathogens (human) in your tank - like vibrio. But - I think there is a huge variability - in the population of organisms - based on the place thats sampled. IMHO - this type of analysis has not yet shown where the 'best' most 'predictive' are of the tank to sample is/are. I am also not at all convinced that 'diversity' - is a goal we should be shooting for - nor is it a goal we can attain. For example. Lets take fish for example. in Theory - every fish we add 'adds diversity' (of a different species). Yet - when One fish eats another - etc etc - diversity declines. IMHO - the same thing happens with microbes. They have niches - they adapt to those - and they resist others. you could make the same example with corals. Add acorapora to a tank full of leather corals. Do you think the acropora will outcompete (or at least maintain itself) - i.e. diversity was added? Or do you think the acropora will not do well. Well - you wanted a discussion. there it is IMHO

 

[Kenneth Wingerter]

What have we learnt from testing microbes? What actions can be resulted from a test result,?

I'd like to think that someday we could develop a standard--based on actual reef habitats--by which we could measure the overall health (or particular developmental stage ) of our system using these analyses. The presence/relative abundance of the major microbial groups could serve as indicators of specific problems/deficiencies in the system. In some cases, certain bacteria or bacterial "foods" could be added in pursuit of this balance.

Maybe just more numbers to chase? Some might say so. But I think this would add an incredibly fascinating aspect to aquarium keeping, particular for advocates of "natural methods." I suppose we have to first determine from surveys of healthy (and maybe unhealthy) actual reefs exactly which bacteria should (and maybe shouldn't) be there. Maybe a Top 20 Microbial Genera to seek (or maybe avoid)?

https://dspace.mit.edu/bitstream/handle/1721.1/106835/248_2013_Article_362.pdf?sequence=1&isAllowed=y

 

[Nano sapiens]

The problem that I see with pursing a 'more perfect biome' (whatever that might be) is how does one determine that? For example, one reef aquarium with relatively low flow and perhaps undersaturated oxygen might have a dominant species (or group of species) that perform nitrification, but another high flow and regularly oxygen supersaturated system might have other dominant specie(s) that perform the same task. Both sets of dominant species can be 'right' for their particular environment, yet be distinctly different microbes.

Going back to the earliest days of reef keeping, they had it right from the beginning Add a bunch of ocean live rock and/or rock from a healthy established system and let the microbes 'do their thing' to achieve a balance over time. Key point there is 'time' which equates to 'patience' which seems to be in short supply these days as many want an optimally functioning reef aquarium in nearly the blink of an eye

 

[MnFish1]

I'd like to think that someday we could develop a standard--based on actual reef habitats--by which we could measure the overall health (or particular developmental stage ) of our system using these analyses. The presence/relative abundance of the major microbial groups could serve as indicators of specific problems/deficiencies in the system. In some cases, certain bacteria or bacterial "foods" could be added in pursuit of this balance.

Maybe just more numbers to chase? Some might say so. But I think this would add an incredibly fascinating aspect to aquarium keeping, particular for advocates of "natural methods." I suppose we have to first determine from surveys of healthy (and maybe unhealthy) actual reefs exactly which bacteria should (and maybe shouldn't) be there. Maybe a Top 20 Microbial Genera to seek (or maybe avoid)?

https://dspace.mit.edu/bitstream/handle/1721.1/106835/248_2013_Article_362.pdf?sequence=1&isAllowed=y

I think this is a nice 'idea' - but it to me - is not realistic. Why? Because there are different bacterial populations on every reef - and - in each tank. And there is no data - AFAIK - that suggests which is 'best'.

 

[ReefBeta]

I don't think we really need to shot for the "best". The more practical use is to detect problem indicator.

I think to build up data set for it, in each submitted test, users need to answer some questions, like if their tank is experiencing dino, cyano, different fish disease, STN, RTN, what corals are doing fine, what are having problem, etc. Then with enough data sample, we might be able to correlate some group of the bacteria to some of those problems in the tank. Then we might be able to find some way to correct that. But is that kind of data being collected in this program? I don't think only collecting data on the microbiome is not that useful, when there aren't enough research to determine what those data mean.

 

[MnFish1]

I don't think we really need to shot for the "best". The more practical use is to detect problem indicator.

I think to build up data set for it, in each submitted test, users need to answer some questions, like if their tank is experiencing dino, cyano, different fish disease, STN, RTN, what corals are doing fine, what are having problem, etc. Then with enough data sample, we might be able to correlate some group of the bacteria to some of those problems in the tank. Then we might be able to find some way to correct that. But is that kind of data being collected in this program? I don't think only collecting data on the microbiome is not that useful, when there aren't enough research to determine what those data mean.

@AquaBiomics is collecting that data

 

[taricha]

Any new info here? Seems the thread has died and it would be good to read some updates.

What have we learnt from testing microbes? What actions can be resulted from a test result,?

There's quite a bit that we've learned from aquabiomics, but I'll point out one that I find fascinating.
https://www.reef2reef.com/ams/the-m...-a-professional-coral-aquaculture-system.749/
In this article, Eli points out that the ammonia and nitrite processing bacteria may be present in large amounts, or in very very small amounts in people's tanks.

EM: One of the things that really stood out about your tank for me is the high levels of nutrient-processing microbes. Ammonia-oxidizing microbes made up almost 8% of your sample, which is higher than about 85% of aquariums I’ve tested, about twice as high as the average sample. Your sample also had high levels of nitrite-oxidizing bacteria (0.9%), which is among the highest of any tanks tested (higher than 96% of samples), and over 3-times higher than the average sample.

This may not come as a surprise, since we expect to find these in a tank with a functional biofilter. But in fact, many established tanks have very low levels of these microbes. In some cases, nitrite-oxidizing bacteria aren’t even detected (although they’re likely still present at low levels).

As I review these surveys from different tanks, lately I’ve been thinking about competition between microbes and other organisms for ammonia. I’m considering the hypothesis that some tanks process most of the ammonia through nitrification, some through assimilation by invertebrates or heterotrophic bacteria, and some through assimilation by algae. In this framework, your tank appears to process most of its ammonia through nitrification, the classic pathway we all learn about when cycling a new tank.

some people have pointed at the low detection of nitrifiers in some aquabiomics samples as a sign that the sampling is not giving a good measure. Maybe...

But maybe not. When you see the crazy fast ammonia uptake rates for algae, it becomes totally believable that in some systems the traditional "cycle" barely happens at all and maybe the role of ammonia consumption has been supplanted by algae.

This idea has been argued before. see here
https://www.reef2reef.com/threads/1...mmonia-is-causing-your-algae-problems.558661/

but aquabiomics has persuasive (to me anyway) data on this hypothesis.

So who eats the ammonia in your system?

 

[MnFish1]

There's quite a bit that we've learned from aquabiomics, but I'll point out one that I find fascinating.
https://www.reef2reef.com/ams/the-m...-a-professional-coral-aquaculture-system.749/
In this article, Eli points out that the ammonia and nitrite processing bacteria may be present in large amounts, or in very very small amounts in people's tanks.


some people have pointed at the low detection of nitrifiers in some aquabiomics samples as a sign that the sampling is not giving a good measure. Maybe...

But maybe not. When you see the crazy fast ammonia uptake rates for algae, it becomes totally believable that in some systems the traditional "cycle" barely happens at all and maybe the role of ammonia consumption has been supplanted by algae.

This idea has been argued before. see here
https://www.reef2reef.com/threads/1...mmonia-is-causing-your-algae-problems.558661/

but aquabiomics has persuasive (to me anyway) data on this hypothesis.

So who eats the ammonia in your system?

I believe its a sampling problem. I cant think of any reason why nitrification/denitrification in a tank would vary based on bacteria -but based on my sampling of several areas of the same tank - and getting completely disparate results - My guess is most of it is sampling issue. Just my opinion.

 

[ReefBeta]

I still didn't get a good idea. When you submit your sample for the microbes test, do you also provide data of what's going on in your tank, like dino/cyno/STN/RTN etc.?

 

[Hans-Werner]

So who eats the ammonia in your system?

Maybe corals? Ammonia is the preferred nitrogen source of corals, not nitrate.

 

[MnFish1]

I still didn't get a good idea. When you submit your sample for the microbes test, do you also provide data of what's going on in your tank, like dino/cyno/STN/RTN etc.?

I haven't done the test for a while - but I believe you can provide information about your tank. He also has (I believe) a database of which bacteria are present in 'good tanks', and 'tanks with problems' (paraphrased) or at least gives you an idea