New article on the microbial communities in saltwater aquariums

[AquaBiomics]

Hi everyone,

 

Most of us in the hobby are aware of the roles microbes play in our tanks, but very little information about these microbes has been available. 

 

I wanted to bring to your attention a recent survey of microbial communities in home aquariums that we've recently completed. This analysis is based on DNA sequencing of water samples from hobbyist tanks. A few of the key findings: 

• The water of established reef tanks contains several hundred different kinds of microbes (400, on average). 
• These include microbes with known roles in maintaining water quality, and also known pathogens. 
• The microbiome of a typical aquarium is dominated by a few families that are also among the most abundant in the ocean. 
• The aquarium microbiome is composed of mostly Bacteria, but some of the few Archaea present have important roles in maintaining water quality. 

 

There are endless questions left to answer in this field... this survey provides a baseline for understanding the typical aquarium microbiome. In future experiments and articles, I'll explore how we can best establish and adjust the microbiome in our aquariums. 

 

You can read more here. I'll be curious to hear what you think!

 

-Eli

 

Quote

The relative abundance of each family in the core microbiome of a typical saltwater aquarium.

 

[Nano sapiens]

Having followed along with oceanic bacterial research for some time now, I was wondering how long it would take until someone applies the same 16s rDNA techniques to our captive reef environments.  And here it is  😊

 

Out of interest, I just ordered a kit to determine the microbial composition of an 11+ year old 12g 'mixed reef' nano aquarium that has no mechanical or chemical filtration, but employs the typical frequent water changes (~10%/week).  Since establishment using Indo-pacific live rock, the system has had minimal input of additional bacteria (other than what has come in on the occasional frag plug, invert or fish).

 

With a large enough sampling size it should be possible to determine if there are any noteworthy differences in the microbiome of quite large vs. quite small systems as both are typically maintained somewhat differently (relative volume/frequency of water changes, type and sophistication of filtration, etc.).

 

Ralph.

 

 

[Xanthine]

Vibrio? Yikes. Thanks for the reminder to wash my hands well after every dip in the tank. And I really need to get some elbow length gloves.

[AquaBiomics]

10 hours ago, Nano sapiens said:

Having followed along with oceanic bacterial research for some time now, I was wondering how long it would take until someone applies the same 16s rDNA techniques to our captive reef environments.  And here it is  😊

 

Out of interest, I just ordered a kit to determine the microbial composition of an 11+ year old 12g 'mixed reef' nano aquarium that has no mechanical or chemical filtration, but employs the typical frequent water changes (~10%/week).  Since establishment using Indo-pacific live rock, the system has had minimal input of additional bacteria (other than what has come in on the occasional frag plug, invert or fish).

 

With a large enough sampling size it should be possible to determine if there are any noteworthy differences in the microbiome of quite large vs. quite small systems as both are typically maintained somewhat differently (relative volume/frequency of water changes, type and sophistication of filtration, etc.).

 

Ralph.

 

 

Thanks for your support, I look forward to seeing the results from your tank!

 

I think you'll be interested to read the study I just completed on establishing tanks using live rock versus dry rock. Since you've watched a successful reef for 12 years started with live rock, it probably wont surprise you to hear that I found high-quality live rock rapidly (within days) establishes a microbiome like that of mature reef tanks, while dry rock shows no evidence of moving in that direction within the first month.

 

I bet your mature tank established with real live rock looks similar to the 'core microbiome' described above... but perhaps with higher diversity, since many of the tanks in my survey were started many years ago with dry rock. Specifically, I predict your tank has both a high diversity and a high balance score (i.e., is similar to the consensus across other mature reef tanks). 

 

I will link the study here as soon as it is available. 

[AquaBiomics]

3 hours ago, Xanthine said:

Vibrio? Yikes. Thanks for the reminder to wash my hands well after every dip in the tank. And I really need to get some elbow length gloves.

I know! I have to say, I came into this from the coral biology side of things. I didn't think about the rich microbial soup that is aquarium water for many years, until like many aquarists I became convinced that the microbial community was important to understanding the health of our tanks. 

 

These days, after learning more about the different human pathogens in Vibrio that survive perfectly well in saltwater.. and the Mycobacterium that have been shown to cause infections in aquarists.... I mus confess I have been taking hygiene a little more seriously around the tank. If I have a cut on my left hand, I am keeping it out of the water these days!

 

With that said, I have yet to detect a known human pathogen in any of the tanks we surveyed. I know they are out there (because there are documented cases of aquarium related infections), but so far we haven't seen them. 🙂

 

[Nano sapiens]

2 hours ago, AquaBiomics said:

Thanks for your support, I look forward to seeing the results from your tank!

 

I think you'll be interested to read the study I just completed on establishing tanks using live rock versus dry rock. Since you've watched a successful reef for 12 years started with live rock, it probably wont surprise you to hear that I found high-quality live rock rapidly (within days) establishes a microbiome like that of mature reef tanks, while dry rock shows no evidence of moving in that direction within the first month.

 

I bet your mature tank established with real live rock looks similar to the 'core microbiome' described above... but perhaps with higher diversity, since many of the tanks in my survey were started many years ago with dry rock. Specifically, I predict your tank has both a high diversity and a high balance score (i.e., is similar to the consensus across other mature reef tanks). 

 

I will link the study here as soon as it is available. 

Looking forward to the article 👍  Do you have previous articles linked on your AquaBiomics website? (I didn't see any link to articles, there). 

 

The work that you are doing here is very interesting and will undoubtedly further our understanding of our captive systems.  The higher the number of data sets, the better, for finding trends, drawing conclusions, etc.,  So I hope that nano reef owners will consider ordered a kit (having the '25% off Black Friday coupon until Cyber Monday' deal on your website should help).

 

The live rock in my nano is over 20 years old now since it came from a previous 55g that I had set up around 1997.  Interestingly, the prevailing 'Internet wisdom' tends to lean toward the idea that older systems will loose bio diversity and that occasional bacterial supplementation is necessary.  The data sets that you are collecting should show if this theory 'holds any water' (excuse the pun) 😉

 

I suspect that my nano *should* have a good amount of bacterial biodiversity.  However, not too long ago I discovered a corroded bolt in one of the rear chambers of this little AIO and I'm not sure if elevated levels of the leached metals has had any negative affect on the microbiome.  I can say that I didn't have any coral issues to speak of, but did notice a moderate increase  in nuisance algae growth which may, or may not, be related.  Overall, the system seems to have tolerated the situation well enough.

 

Ralph.

 

[AquaBiomics]

 

23 hours ago, Nano sapiens said:

Looking forward to the article 👍  Do you have previous articles linked on your AquaBiomics website? (I didn't see any link to articles, there). 

 

The work that you are doing here is very interesting and will undoubtedly further our understanding of our captive systems.  The higher the number of data sets, the better, for finding trends, drawing conclusions, etc.,  So I hope that nano reef owners will consider ordered a kit (having the '25% off Black Friday coupon until Cyber Monday' deal on your website should help).

 

The live rock in my nano is over 20 years old now since it came from a previous 55g that I had set up around 1997.  Interestingly, the prevailing 'Internet wisdom' tends to lean toward the idea that older systems will loose bio diversity and that occasional bacterial supplementation is necessary.  The data sets that you are collecting should show if this theory 'holds any water' (excuse the pun) 😉

 

I suspect that my nano *should* have a good amount of bacterial biodiversity.  However, not too long ago I discovered a corroded bolt in one of the rear chambers of this little AIO and I'm not sure if elevated levels of the leached metals has had any negative affect on the microbiome.  I can say that I didn't have any coral issues to speak of, but did notice a moderate increase  in nuisance algae growth which may, or may not, be related.  Overall, the system seems to have tolerated the situation well enough.

 

Ralph.

 

I made them look more like blog posts than scientific articles, in hopes of reaching a broader audience. But I fear after so many years in Academia I'm having to leran how to not write like a scientist. 

 

I've got two articles / blog posts available currently, based on surveys and analysis I've done at AquaBiomics:

1. The typical microbiome of a saltwater aquarium

2. How aquarium microbiomes differ

 

My next one describes a month long experiment starting experimental nano tanks with live rock versus dry rock, I'll link it here as soon as its live. 

 

You mention changes in diversity over time. Long term time series are still a work in progress but here is a figure from the first month after establishing my experimental tanks... it's a pretty dynamic picture in the first month but I would not say theres any evidence for decline in diversity over time. (I have heard that idea too.) I will be curious to see how repeated samples turn out over a longer time series. 

 

And I have one sample in my next batch from a >40 year old tank, can't wait to see what that looks like!

 

[Nano sapiens]

10 hours ago, AquaBiomics said:

I made them look more like blog posts than scientific articles, in hopes of reaching a broader audience. But I fear after so many years in Academia I'm having to leran how to not write like a scientist. 

 

I've got two articles / blog posts available currently, based on surveys and analysis I've done at AquaBiomics:

1. The typical microbiome of a saltwater aquarium

2. How aquarium microbiomes differ

 

My next one describes a month long experiment starting experimental nano tanks with live rock versus dry rock, I'll link it here as soon as its live. 

 

You mention changes in diversity over time. Long term time series are still a work in progress but here is a figure from the first month after establishing my experimental tanks... it's a pretty dynamic picture in the first month but I would not say theres any evidence for decline in diversity over time. (I have heard that idea too.) I will be curious to see how repeated samples turn out over a longer time series. 

 

And I have one sample in my next batch from a >40 year old tank, can't wait to see what that looks like!

 

Great, thanks for the links. 

 

This caught my attention:

 

Now that microbiome testing is readily available for aquariums, it will be interesting to learn how deliberate manipulation of the nutrient profiles in aquariums can be used to adjust their microbiomes.

 

In my own aquariums, I have noticed subtle differences in the fauna and flora depending on the type(s) of food being fed.   For example, if I feed mostly frozen foods such as LRS or Rod's Food, the organisms growing on the back wall tend to be somewhat different in color and texture compared to those that I see if I feed predominantly dried food.  Stands to reason that the bacterial compositions could be influenced by the ratio and abundance/lack of certain nutrients and elements.

 

As for that >40 year old tank, might that be Paul B's ancient reef aquarium? 

[AquaBiomics]

33 minutes ago, Nano sapiens said:

I have noticed subtle differences in the fauna and flora depending on the type(s) of food being fed.   For example, if I feed mostly frozen foods such as LRS, the organisms growing on the back wall tend to be somewhat different in color and texture compared to those that I see if I feed predominantly dried food.  Stands to reason that the bacterial compositions could be effected due to the ratio and abundance/lack of certain nutrients and elements.

Yes! There is a lot of interest in (and money being spent on) cultured bacterial products, but most bacteria cannot be cultured... however, we know that the nutrients available in natural seawater determine the kinds of bacteria that bloom. I think this is the most productive area for us to focus on, in terms of adjusting our tanks microbiomes. 

 

Whether its pure compounds (like amino acids) or complex mixtures (like pellets or blended seafood slurries) we are feeding the microbial community every time we feed the tank... I bet this will be one of the most effective ways to manipulate the community. 

[Nano sapiens]

47 minutes ago, AquaBiomics said:

Yes! There is a lot of interest in (and money being spent on) cultured bacterial products, but most bacteria cannot be cultured... however, we know that the nutrients available in natural seawater determine the kinds of bacteria that bloom. I think this is the most productive area for us to focus on, in terms of adjusting our tanks microbiomes. 

 

Whether its pure compounds (like amino acids) or complex mixtures (like pellets or blended seafood slurries) we are feeding the microbial community every time we feed the tank... I bet this will be one of the most effective ways to manipulate the community. 

I was just looking at your 'Register a Sample' page.  How about a section for foods fed over a week's time, something like 'radio buttons' for 'Dry Food', 'Frozen Food' and 'Fresh/Live Food'.  When any of the radio buttons are clicked, a percentage scale (10%, 20%, 30%, etc.) pops up and allows the user to make a selection with a combined total that must equal 100%.  A user entry field could be provided for each of these three categories (for those so inclined to specify the type/brand of food fed).  Capturing this data *could* provide interesting insights into why some aquariums have 'typical' bacterial profiles, while others are well outside the norm.