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

[brandon429]

Never knew of day night differences NS nice find

 

[Nano sapiens]

Never knew of day night differences NS nice find

While I had had a passing thought that this might be a possibility, studies have shown that in oceanic waters around the world changes in the microbiome day and night are relatively small. However, tropical reef ecosystems are special cases.

For me, the obvious question is how much would the microbial composition have differed if I had collected my reef aquarium sample at say 7 pm (near the end of my lighting cycle) instead of in the dark at the 7 am? Based on excerpts from this article, the high percentage of Pelagibacteraceae in my sample suggests that this is quite possibly due to when the sample was taken (Pelagibacteracae was one of the most common families found a night).

Would be most interesting to return 2 samples to Aquabiomics, maybe one from the middle of the aquarium's night and one from the mid day light cycle.

Lastly, the article mentions the Psychrobacter genus (family Moraxellaceae, class Gammaproteobacteria) as dominating the microbial day communities. I do not see the Moraxellaceae family in the Aquabiomic's 'Core Microbiome'. It would be odd if this family is not represented in our reef aquaria, so I'm wondering if it shows up in sampled aquaria outside of the Core Microbiome group of 19?

Curious to hear what Eli thinks of all this.

Ralph.

 

[Nano sapiens]

Lastly, the article mentions the Psychrobacter genus (family Moraxellaceae, class Gammaproteobacteria) as dominating the microbial day communities. I do not see the Moraxellaceae family in the Aquabiomic's 'Core Microbiome'. It would be odd if this family is not represented in our reef aquaria, so I'm wondering if it shows up in sampled aquaria outside of the Core Microbiome group of 19?

Ralph.

Unable to edit previous post...

Found Moraxellaceae weakly represented in Aquabiome's 'typical' reef aquarium graphic.

 

[Mortie31]

I took a stroll around the Web and found this fascinating paper directly in line with the question 'What does a healthy, natural reef water column microbial community look like?'

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

This research deals specifically with the microbial communities on four of the Southern Line Islands (some of the most pristine coral reef communities in the world). Not only the composition of the microbial community is determined (some interesting microbial differences from our reef systems stand out), but it also answers the question of how does the microbial community differ in a 24 hr period? Turns out, the difference is 'day and night', literally! The daytime community makeup is quite different from the one at night. In fact, the difference is more pronounced from day to night in one specific spot than from one island to another island.

I think it's safe to presume that the day and night microbiome in our reef systems also undergoes a day-to-night change. Would the changes be as pronounced? More pronounced? How would the microbial families makeup/percentages be different at night vs. day?

Interesting stuff!

Ralph.

This is very interesting, and I think highlights just how complex and variable microbiomes are, not only diurnal variance but location and possibly seasonal shifts as well... a concern to me the, the question again of what is; typical or normal .. is it impossible to answer that? In the ocean let alone our tanks, I think there is decades of research ahead..

 

[AquaBiomics]

While I had had a passing thought that this might be a possibility, studies have shown that in oceanic waters around the world changes in the microbiome day and night are relatively small. However, tropical reef ecosystems are special cases.

For me, the obvious question is how much would the microbial composition have differed if I had collected my reef aquarium sample at say 7 pm (near the end of my lighting cycle) instead of in the dark at the 7 am? Based on excerpts from this article, the high percentage of Pelagibacteraceae in my sample suggests that this is quite possibly due to when the sample was taken (Pelagibacteracae was one of the most common families found a night).

Would be most interesting to return 2 samples to Aquabiomics, maybe one from the middle of the aquarium's night and one from the mid day light cycle.

Lastly, the article mentions the Psychrobacter genus (family Moraxellaceae, class Gammaproteobacteria) as dominating the microbial day communities. I do not see the Moraxellaceae family in the Aquabiomic's 'Core Microbiome'. It would be odd if this family is not represented in our reef aquaria, so I'm wondering if it shows up in sampled aquaria outside of the Core Microbiome group of 19?

Curious to hear what Eli thinks of all this.

Ralph.

Hi Ralph,

Really interesting find. I always find it amazing how day/night cycles affect every level of life, not just behavior... corals turn on and off different genes, and the composition of microbial populations can change, sometimes by a lot.

A few overall thoughts
1. We absolutely should measure this in aquariums, it is on the list. I don't have data in hand to answer the question directly.
2. Most of the samples in the database were collected during daylight so I have limited power to test for these effects in existing data.
3. In terms of the specific families you mention, the patterns we're seeing so far in aquariums don't appear to be driven by the day/night effects described here.

To get into specifics -- the family Moraxellaceae is found in most tanks sampled (61%) but typically at low levels (0.3% of the community on average). In some tanks this includes Pyschrobacter, but this genus was only found in 8% of tanks tested so far. Most of the samples in the database were taken during the day, based on the info logged by users when they registered samples.

On the other end, Pelagibacteraceae. In a database composed mostly of daytime samples, we find this group in most tanks (86%), sometimes at very high levels (up to 60%). I personally collected samples during midday that were highly dominated by Pelagibacteraceae. So I do not think the dominance of this group in the 'typical aquarium microbiome' is likely to result from the day/night patterns described here.

That said, I'd bet there are detectable day vs night differences in the aquarium microbiome. And this article will provide a nice framework for comparing them with day vs night differences on a natural reef.

 

[AquaBiomics]

This is very interesting, and I think highlights just how complex and variable microbiomes are, not only diurnal variance but location and possibly seasonal shifts as well... a concern to me the, the question again of what is; typical or normal .. is it impossible to answer that? In the ocean let alone our tanks, I think there is decades of research ahead..

Decades of research ahead? Absolutely.

This question (what does it mean to deviate from the 'typical' microbiome?) is one I think about a lot and there are lots of unknowns here.

But consider this. Aquariums operated by different people converge on a similar community (see my initial survey here). Other tanks deviate from this 'consensus' in a few predictable ways. I interpret this clustering pattern to mean that there is a characteristic microbial community associated with established reef tanks.

So what does it mean to deviate from this community? It seems very likely that there are multiple possible communities that could support a stable and resilient ecosystem in the aquarium. We've absolutely seen successful tanks with atypical communities. So I'm definitely not saying any deviation from the norm is a problem.

My point is only that we can ask, "does my tank have a typical profile or an atypical profile" and get a clear answer. Observations of atypical profiles immediately raise the question "why is the community in my tank different?" and this is where we step off into an area where there are few clear answers. Yet.

I will also add that my followup discussions with people whose tanks have atypical profiles have often uncovered interesting pieces of info about how the tank is run (e.g. dosing live phytoplankton or regularly feeding live earthworms). Every reef keeper is captain of his or her own ship and many are running interesting experiments in their tanks that seem likely to contribute to these differences.

 

[Nano sapiens]

Most of the samples in the database were taken during the day, based on the info logged by users when they registered samples.

Thanks for the detailed response, Eli. Exciting to see this whole new chapter of reef aquarium microbiology unfolding.

In response to your observation that most samples were taken during the day, my thought is that the most important data point would be when the sample was taken in relation to the lighting cycle (assuming light waves and/or photosynthesis is the catalyst for the day/night change in microbial composition as seen on the natural reef).

As an example, I prepared my sample at 7 am, but my 8 hour lighting cycle only starts at 12 pm (noon). So from my system's point of view, it was 11 hours into a 'dark cycle' and 5 hours away from the beginning of the 'light cycle'.

Ralph.

 

[Huskymaniac]

@AquaBiomics. Hey Eli, gotta a question for you. Any recommendation on how to boost some of these populations to that were lower in my tank than a typical tank? Both of my tank do employee large UV sterilizers plumbed online and I wonder how much of that is responsible for the lower scores? The below comment was what I was referencing. Have any of the supplements you tested actually have these specific bacteria in there?

Both tanks showed low balance scores, indicating that the balance of microbial families was very different in your tanks than in the typical tank. Please note this does not necessarily mean there is anything wrong with your tank - it just puts a number on how similar or different your tank is from others. In your case, both are pretty different.

To explore the reasons for these low balance score we can look at the community barplots (part 2). Both tanks are very low in Pelagibacteracea, which are dominant in the open ocean, a major part of the typical reef tank microbiome, and are specialized for low nutrient conditions. This happens in many tanks, and I'm not saying its a problem. But it is a common difference between some tanks and the microbiome of a natural reef. Both tanks are also low in Flavobacteriacea, and your 750 is also low in Alteromonadaceae.

 

[AquaBiomics]

@AquaBiomics. Hey Eli, gotta a question for you. Any recommendation on how to boost some of these populations to that were lower in my tank than a typical tank? Both of my tank do employee large UV sterilizers plumbed online and I wonder how much of that is responsible for the lower scores? The below comment was what I was referencing. Have any of the supplements you tested actually have these specific bacteria in there?

Both tanks showed low balance scores, indicating that the balance of microbial families was very different in your tanks than in the typical tank. Please note this does not necessarily mean there is anything wrong with your tank - it just puts a number on how similar or different your tank is from others. In your case, both are pretty different.

To explore the reasons for these low balance score we can look at the community barplots (part 2). Both tanks are very low in Pelagibacteracea, which are dominant in the open ocean, a major part of the typical reef tank microbiome, and are specialized for low nutrient conditions. This happens in many tanks, and I'm not saying its a problem. But it is a common difference between some tanks and the microbiome of a natural reef. Both tanks are also low in Flavobacteriacea, and your 750 is also low in Alteromonadaceae.

Interesting. I have relatively few tanks in the database that use UV sterilizers, 7 so far including yours. But on reviewing them, I see that yes, all of these have very low levels of Pelagibacteracea like yours. (So do some other tanks without UV sterilizers... but All tanks with UV appear to match this pattern).

Its an intriguing idea because Pelagibacteraceae are free-living bacteria in the water column, exactly the kind of thing we'd expect to be removed by a UV sterilizer.

Perhaps the database has grown enough for another round of statistical tests! Every now and then I look for associations between aquarium practices and microbiome patterns. e.g. are there any differences associated with use of a UV sterilizer. Usually I come to the conclusion we don't have enough samples yet. But this is worth another look, next time I have some time to dedicate to analysis.

In terms of how to increase this group (should you choose to),
1. I don't have data in hand yet for the contents of the various bottled products but the few tests available that compare tanks with and without bacteria show no evidence they increase this group.
2. When I added live sand and mud to two of my established tanks I got substantial increases in Pelagibacteracea (one of them also increased in Flavobacteriaceae)

BUT, I am uncertain how to proceed with any suggestions based on inoculating new free-living microbes in the system when there is a UV sterilizer in operation. I'm a newbie when it comes to constant use of UV sterilizers, my only experience with them has always been to initially sterilize water for batch cultures. It just seems this is a factor to think about especially if we are asking whether the UV could be driving this pattern.

Is it safe for the rest of your system (ignoring the microbes) if you turn off the UV for a while? Does anyone use UV sterilizers intermittently?

 

[Huskymaniac]

Interesting. I have relatively few tanks in the database that use UV sterilizers, 7 so far including yours. But on reviewing them, I see that yes, all of these have very low levels of Pelagibacteracea like yours. (So do some other tanks without UV sterilizers... but All tanks with UV appear to match this pattern).

Its an intriguing idea because Pelagibacteraceae are free-living bacteria in the water column, exactly the kind of thing we'd expect to be removed by a UV sterilizer.

Perhaps the database has grown enough for another round of statistical tests! Every now and then I look for associations between aquarium practices and microbiome patterns. e.g. are there any differences associated with use of a UV sterilizer. Usually I come to the conclusion we don't have enough samples yet. But this is worth another look, next time I have some time to dedicate to analysis.

In terms of how to increase this group (should you choose to),
1. I don't have data in hand yet for the contents of the various bottled products but the few tests available that compare tanks with and without bacteria show no evidence they increase this group.
2. When I added live sand and mud to two of my established tanks I got substantial increases in Pelagibacteracea (one of them also increased in Flavobacteriaceae)

BUT, I am uncertain how to proceed with any suggestions based on inoculating new free-living microbes in the system when there is a UV sterilizer in operation. I'm a newbie when it comes to constant use of UV sterilizers, my only experience with them has always been to initially sterilize water for batch cultures. It just seems this is a factor to think about especially if we are asking whether the UV could be driving this pattern.

Is it safe for the rest of your system (ignoring the microbes) if you turn off the UV for a while? Does anyone use UV sterilizers intermittently?

Eli,
May also be worth looking at those who dose h2o2 and use ozone as they would likely fall into the same category of UV. I can run it intermittently but assuming once it's back ok n would just zap everything again anyways. It's also one of the things I swore I would always keep running 24/7 after my hand Infection.

 

[AquaBiomics]

Eli,
May also be worth looking at those who dose h2o2 and use ozone as they would likely fall into the same category of UV. I can run it intermittently but assuming once it's back ok n would just zap everything again anyways. It's also one of the things I swore I would always keep running 24/7 after my hand Infection.

Yeah, I can understand that, that infection would be a strong motivator to keep the UV on!

And I see your point that perhaps intermittent use would not make any difference. Honestly I havent run UV in a recirculating system so I'm wildly speculating in terms of how to adjust it. Just thinking that if Pelagibacteraceae and other free living bacteria are low because of the UV, its hard to ignore reducing the UV as a possible strategy for increasing those groups. I certainly understand the hesitation to do that given the history of infection from one of the tanks.

 

[AquaBiomics]

Can you rush the Vibrant sampling along, please?

Just wanted to let you know, this is definitely happening. Especially now that Jeff @UWC has generously offered to supply the product for these experiments (Thanks again, Jeff!). I'm going to dedicate a replicated set of tanks for this in my next round.

I'd like to document the effects generally (in addition to the effects on the microbiome). I'll search the forums on this question, but thought I'd ask here too -- what is a consistently observed and measurable benefit of Vibrant? I haven't used it myself. I ask, because if for example the answer were bubble algae, I would need to add these to my experimental tanks before the experiment to make it a fair test.

 

[fermentedhiker]

Just wanted to let you know, this is definitely happening. Especially now that Jeff @UWC has generously offered to supply the product for these experiments (Thanks again, Jeff!). I'm going to dedicate a replicated set of tanks for this in my next round.

I'd like to document the effects generally (in addition to the effects on the microbiome). I'll search the forums on this question, but thought I'd ask here too -- what is a consistently observed and measurable benefit of Vibrant? I haven't used it myself. I ask, because if for example the answer were bubble algae, I would need to add these to my experimental tanks before the experiment to make it a fair test.

There is a huge Vibrant thread on here. Be prepared to take a significant amount of time to get through it . My understanding from UWC posts are that it's a combo of two different types of bacteria(not sure how many species) a sludge digester , and one that actively attacks algae. For benefits I saw; Clearer water, Killed hair algae outbreak, stopped spread of bubble algae(I didn't use it long enough to kill that), On the con side, I didn't see much nutrient reduction from the sludge digester activity, water clearing was followed by a significant drop in pod population(I presume it disrupted part of the food chain that they depended on). Damages macro algae in refugiums/ats/reactors although it didn't seem to hurt mine(again I didn't run it very long after I got the hair algae eradicated). Also I found my corals seemed to get mad as I continued dosing at the maintenance dose. It took two or three days after stopped dosing for them to go back to normal so that is an anecdotal conclusion at best.

 

[Huskymaniac]

Just wanted to let you know, this is definitely happening. Especially now that Jeff @UWC has generously offered to supply the product for these experiments (Thanks again, Jeff!). I'm going to dedicate a replicated set of tanks for this in my next round.

I'd like to document the effects generally (in addition to the effects on the microbiome). I'll search the forums on this question, but thought I'd ask here too -- what is a consistently observed and measurable benefit of Vibrant? I haven't used it myself. I ask, because if for example the answer were bubble algae, I would need to add these to my experimental tanks before the experiment to make it a fair test.

Ime it kills algea but causes blooms of nacteria such as cyano and spirulina so I have been hesitant to use it.

 

[ElussssvReefSD]

Hi Eli,

I have a question regarding the total bacterial load in samples you've received thus far. If I'm understanding the results that have been posted thus far correctly, this test provides the relative abundance of different types of bacteria and measures the samples' total diversity using DNA fragments more or less. However, I am curious to know if your testing method also has the ability to estimate a gross total bacterial load present in a given sample of water, not just the ratio of one to another.

The reason I ask is that I am currently trying to decide whether to plumb a large UV sterilizer into my new build in order to decrease the overall circulating bacterial load in the water column. I do understand that the use of UV can be somewhat controversial due to many different factors which I don't want to get into in this thread, but I would be curious to see if this testing method could also be used to quantify how effective a UV sterilizer is in a given setup.

Unlike many of you in this thread, please understand that I am not a biologist or scientist, so I apologize if this question is totally off-base. I just find this topic super-interesting and want to learn more about the microbiome of our little glass boxes.

 

[Nano sapiens]

Unlike many of you in this thread, please understand that I am not a biologist or scientist, so I apologize if this question is totally off-base. I just find this topic super-interesting and want to learn more about the microbiome of our little glass boxes.

Not to worry, most of us are not (myself included). However, that doesn't mean that we can't contribute with relevant, probing questions or steer the endeavor to better understand out aquariums' microbiomes in unexpected directions with some 'out-of-the-box' thinking

 

[AquaBiomics]

Hi Eli,

I have a question regarding the total bacterial load in samples you've received thus far. If I'm understanding the results that have been posted thus far correctly, this test provides the relative abundance of different types of bacteria and measures the samples' total diversity using DNA fragments more or less. However, I am curious to know if your testing method also has the ability to estimate a gross total bacterial load present in a given sample of water, not just the ratio of one to another.

The reason I ask is that I am currently trying to decide whether to plumb a large UV sterilizer into my new build in order to decrease the overall circulating bacterial load in the water column. I do understand that the use of UV can be somewhat controversial due to many different factors which I don't want to get into in this thread, but I would be curious to see if this testing method could also be used to quantify how effective a UV sterilizer is in a given setup.

Unlike many of you in this thread, please understand that I am not a biologist or scientist, so I apologize if this question is totally off-base. I just find this topic super-interesting and want to learn more about the microbiome of our little glass boxes.

The answer is that to measure this with any precision requires either additional equipment or processing time. So it's not part of the usual analysis I run on client samples.

But I do think it's useful information, both for interpreting changes in the ratios and for evaluating the effects of things like UV or carbon dosing. Not an off-base question at all. Its on the list of planned future additions to the service.

If someone had a pair of samples and wanted to compare the relative abundance of microbes in them, I can measure this using a PCR approach. If there is a particular reason to want this information (like measuring the effects of a UV sterilizer) I'd be happy to run this in addition to the sequencing service. It's hands-on time intensive, so it doesnt scale well to running on the whole batch, but no problem for a small number of samples.

 

[Huskymaniac]

After reviewing the options I chose a two step process that can be done with equipment on hand. It will take a month to order reagents and test each step, in principle its a rapid assay when the materials are on hand and tested. So give me a month this time. A week in the future if we ever wanted to retest a tank.

Its an important enough bug that this was a good one to focus on. And the general approach here (confirming results from DNA sequencing with a rapid test I can complete in-house) could be useful for a few cases like this.

Hey Eli, just checking to see how everything is going. Still looking at next week sometime?

 

[AquaBiomics]

Hey Eli, just checking to see how everything is going. Still looking at next week sometime?

Sent you a PM. Yes, maybe even sooner.

The biggest bottleneck in my process is that after sending it to the sequencing facility it's out of my hands and subject to other peoples' timing or technical difficulties. I'm looking into purchase of a new instrument which would both (a) remove this uncertainty and (b) reduce the overall processing time by 1-2 weeks. But this purchase is big enough that financing it will require some additional work.

For now we operate the same way as most people in the DNA sequencing world - prepare out samples then send them to the sequencing facility. I dream about the day I can remove that step and keep it all in house.

 

[ScottB]

BUT, I am uncertain how to proceed with any suggestions based on inoculating new free-living microbes in the system when there is a UV sterilizer in operation. I'm a newbie when it comes to constant use of UV sterilizers, my only experience with them has always been to initially sterilize water for batch cultures. It just seems this is a factor to think about especially if we are asking whether the UV could be driving this pattern.

Is it safe for the rest of your system (ignoring the microbes) if you turn off the UV for a while? Does anyone use UV sterilizers intermittently?

Perhaps a gross generalization, but anecdotally I would suggest that the answer depends on what problem the UV is intended to solve.
- For fish parasites/pathogens, people run them full time, all the time. Plumbed in line.
- For dinoflagellates, UVs are temporarily hung on the back/side of the affected display, pumping from and returning to the display.

When I send you my samples, one will have UV and the other will not. Will be interesting to see differences.