Effects of live sand & mud on the microbial communities in my tanks (updated with new data)

[lexinverts]

Thanks for the kind words. I feel kinda bad because it looks like the vendor I recommended has been sold out for a while now. So I am not sure how practical my recommendation was!

Still, plenty of other live sand vendors out there in principle, and I know that FloridaPets does restock periodically, I've seen their inventory update perhaps weekly.

In terms of sandstorms, I should clarify that one of the tanks I treated here is bare bottom display, with live -ish rock and now live sand and mud in the refugium. I prefer sand bottoms in display tanks but this is a frag tank system (2 frag tanks with a sump) and I prefer to run those without sand in the display. So the effects of live sand/mud don't require having sand in the display.

Floridapets.com now has Keys live mud and Keys live sand back in stock! I just ordered some.

 

[AquaBiomics]

I've updated the original post to include data from my other control tank, which wasn't available when I original wrote this. All the same conclusions are still supported, now with replication.

I also recalculated the diversity percentiles to compare them all with the current version of the database. This correction makes the diversity benefits of the treatment more apparent.

Most interesting, in the process of reviewing these data I also noticed something I didn't catch the first time: this treatment substantially improved the levels of Nitrite-Oxidizing Bacteria (NOB) in the treated tanks, which were initially not detectable. That is a pretty nice benefit!

I see that FloridaPets.com has already sold out of the live mud again Glad I got mine when I did.

 

[lexinverts]

I've updated the original post to include data from my other control tank, which wasn't available when I original wrote this. All the same conclusions are still supported, now with replication.

I also recalculated the diversity percentiles to compare them all with the current version of the database. This correction makes the diversity benefits of the treatment more apparent.

Most interesting, in the process of reviewing these data I also noticed something I didn't catch the first time: this treatment substantially improved the levels of Nitrite-Oxidizing Bacteria (NOB) in the treated tanks, which were initially not detectable. That is a pretty nice benefit!

I see that FloridaPets.com has already sold out of the live mud again Glad I got mine when I did.

If you click on the Keys Live Mud icon, it shows that it is still in stock.

 

[BeejReef]

I just took a flyer on some myself.

Have any of your tests shown whether the microbial diversity is long-lasting, or it the sort of thing you have to refresh now and again?

 

[AquaBiomics]

I just took a flyer on some myself.

Have any of your tests shown whether the microbial diversity is long-lasting, or it the sort of thing you have to refresh now and again?

Its a question I wonder about too. I test my home tanks every month or two so I will update the post when I see the next results from these tanks. I'll be curious to see how long the benefit lasts.

 

[Russell Casey]

[updated Feb 17, 2020 to include data from an additional tank]

One of the most common questions I get is "If there's something I don't like about my aquarium's microbiome, what can I do about it?" In this thread I'll describe my experience with this question on my own home tanks.

The punchline is this: my experience suggests that live sand and mud provide a very low-cost way to adjust the microbial communities in established reef tanks.

Since this describes my home display tanks, which differ from each other in several ways, this is more of an anecdote than a formal experiment. But I figured since it provides a realistic example of what a hobbyist can do with this in a real world setting, it would be worth sharing anyway. (I'll update the thread in the future as I continue to monitor the communities in these tanks)

What I didn't like in my initial tests
The microbial communities in several of my home display tanks were not as diverse as I wanted, and were dominated by different bacterial families than the typical pattern I'd seen in healthy reef tanks. I wanted to change that.

I have four systems in my home (each includes 2 or more tanks so I count by systems instead of tanks). Three of them showed communities dominated by Alteromonadaceae. This was a pattern I've seen in many tanks I've sampled. It's one of the most common ways for a tank to deviate from the "typical" community (i.e., the average of healthy reef tanks I've sampled) -- a bloom of Alteromonadaceae. I don't have evidence showing this group causes a problem. I just know it's a difference from the community I wanted in most of my tanks.

Except Tank B. It has the highest levels of Alteromonadaceae. But it is also an unusual tank that is finally behaving like I want it to, after much work. Its unusual (among my systems) because it has no macroalgal refugium. Instead, I have lots of macroalgae in the display. Its mostly Gracilaria hayi with some other assorted reds, I'm terrible at algal ID. The tank is macroalgae, soft corals, and fish. Most of the display tank has low to moderate light and low to moderate flow... I call it the lagoon tank (Tank B, here).

I used to struggle with cyano problems in Tank B, which after a month or two of nitrate dosing to 5 ppm finally went away. Since then I've monitored nitrates and dosed as needed to maintain 5-10 ppm. Whatever microbial community is growing in that algal lagoon is working. I didn't want to disturb it, so I made that tank one of the controls, and didn't change anything.

I decided to experiment with the microbial communities in the other two tanks (A and D) to see how I could adjust them to make them more like the typical reef tank profile. I wanted higher diversity, less Alteromonadaceae, and more Pelagibacteracea and Flavobacteriaceae. Consider it purely personal preference, since they are my personal tanks. And I deliberately didnt change the other two systems, to serve as controls.

What I added to the tanks
For a variety of reasons I wanted to experiment with low-cost options for these tanks. 1) I'm naturally a cheapskate / bargain hunter in just about all aspects of life. 2) especially when it comes to optional expenses for a hobby. 3) when I've advocated live rock others have rightly ask, "this stuff is expensive -- aren't there any cheaper options?"

Here is what I found: live mud and sand at FloridaPets.com, collected in the Florida Keys. Please note I am not affiliated with this product in any way other than as a happy customer. I'm sure there are plenty of other suppliers, and I haven't done any kind of comparison between sources. It would be very interesting to compare sources... I am sure they all have different collection sites.

I bought 1 cup of the Live Keys Sand and 1 cup of the Live Mud for a grand total of $12.99. The material was shipped USPS Priority and looked and smelled good on arrival. I mean, the mud smelled like typical marine mud, but a normal smell, not a nasty decaying smell. I'm sorry I don't have a vocabulary like wine tasters' to describe this. I've just spent a lot of time around marine mud and the material looked and smelled reassuringly like normal ocean-smelling mud and sand. So in it went.

I split it in half, and added half to each of two tanks. I added it to the drain chamber of my sumps, which flows downward, providing the best chance of letting it settle out instead of blowing around the tank. I lowered it under the water surface to the bottom in a little tupperware container, then emptied the mud and sand into the chamber gently, to minimize mixing. That was it. Took about 5 minutes total. It created a little cloudiness when I added it that night, which was cleared up by morning.

Changes I observed in the tanks' microbiomes

I tested the tanks again about a week and a half after adding the sand and mud. The treated tanks initially ranged from low-diversity to very low diversity. After the addition of live sand & mud, these tanks ranked among the most diverse of tank I've sampled so far.

Treatment (Tank name)	Diversity Before (Percentile)	Diversity After (Percentile)
Control (Tank B)	151 (0.06)	360 (0.57)
Control (Tank C)	156 (0.08)	332 (0.47)
+Mud (Tank A)	201 (0.15)	544 (0.88)
+Mud (Tank D)	72 (0.00)	576 (0.92)

[edit: I've re-analyzed all samples so that the percentiles are calculated relative to the current database. A careful reader may notice that some percentile values have changed as a result.]




However, the untreated tanks also showed a smaller increase in diversity, showing typical diversity in the later sample. This remained well below the high diversity levels of the +Mud tanks.

Since I transfer small amounts of water between tanks daily during feeding, I speculate that this increase in diversity in the control tank may reflect transfer from +Mud tanks (remember, I treated this one like a hobby rather than an experiment. My tank habits predate my interest in aquarium microbiology!)

The changes in communities were even more striking. The systems treated with live sand & live mud had obvious reductions in Alteromonadaceae. Both of them also showed increased levels of Pelagibacteraceae, and Tank D also showed increased Flavobacteriaceae.

Sampled collected from the control tanks remained similar to the initial samples. In both control tanks, the dominant family remained unchanged (Alteromonadaceae for tank B, Pelagibacteraceae for tank C). The relative stability of communities in the control tanks increases our confidence in concluding that the changes in treated tanks were caused by the addition of live sand and mud.

One of the most interesting findings is a recent addition. In revisiting the new data for tank C I realized I had previously overlooked an important benefit of this treatment. Live sand & mud increased the amount of nitrite-oxidizing bacteria (NOB) in the treated tanks. See the following figure, which simply extracts the NOB data from standard AquaBiomics tests before and after the change in each tank.

It's a pretty dramatic change: tanks A and D had no detectable NOB before the addition of live sand & mud, but had normal to high levels after adding this material. The untreated tanks showed no such increase during the same time -- in fact, one of them (B) was initially present at low levels and undetectable in the later sample.

Tank D also showed a large increase in ammonia-oxidizing microbes (AOA & AOB). This change (not shown) was less impressive visually because all samples had detectable levels of AOA & AOB before the addition of live sand & mud.

Conclusions
It probably wouldnt surprise anyone that adding live sand and mud to the aquarium affects the community. I doubt anyone could have predicted exactly which changes would occur from adding this material. I sure couldn't have.

I've summarized the effects of these treatments in the following table, to let the reader draw their own conclusions.

	Untreated		Live sand & mud
	Tank B	Tank C	Tank A	Tank D
Change in dominant family	no	no	yes	yes
Alteromonadaceae	increased	increased	decreased	decreased
Pelagibacteraceae	decreased	decreased	increased	increased
Nitrite-oxidizing bacteria	decreased	unchanged	increased	increased

I conclude that the treatments accomplished got exactly the kind of changes I was hoping for -- I got lucky.




Did they improve the health of the tanks? That's another question and a more difficult one. The tanks are so different it would be hard to compare them in terms of benefits. I will say that both tanks have showed marked reductions in problem algae. Tank A had cyano on the sandbed, and the frag tray in Tank B had a variety of problem algae. Subjectively, without any measurements, both have improved. But I lack controls for that effect (i.e. untreated tanks with algal problems) so we can't attribute those benefits to the treatment. Certainly no harm done, and subjectively both tanks are doing well and arguably better than before.

I make no strong claims about any benefits on the general health of the tanks. Its too soon to say. But I was happy with the effects on the microbial communities themselves, and thought I'd share.

 

[Big E]

What part of the bacterial community is being skimmed out?

What happens to biodiversity with large water changes?

www.advancedaquarist.com/blog/microbe-populations-in-saltwater-aquariums-highly-dynamic

A lot of good info in here on bacterial counts

My systems are mainly acropora so I have always been more focused on the bacteria that ride on of surface of each coral and are of paramount importance vs water born levels.

I think there are a few other articles out there concerning bacteria levels in aquariums.

I'm probably more interested in dosing ammonia vs using bottles of bacteria or live sand.
================================

On another note--------- a product like Siporax has a much higher bacterial storage level than live rock and takes up a lot less space.

 

[AquaBiomics]

What part of the bacterial community is being skimmed out?

What happens to biodiversity with large water changes?

www.advancedaquarist.com/blog/microbe-populations-in-saltwater-aquariums-highly-dynamic

A lot of good info in here on bacterial counts

My systems are mainly acropora so I have always been more focused on the bacteria that ride on of surface of each coral and are of paramount importance vs water born levels.

I think there are a few other articles out there concerning bacteria levels in aquariums.

I'm probably more interested in dosing ammonia vs using bottles of bacteria or live sand.
================================

On another note--------- a product like Siporax has a much higher bacterial storage level than live rock and takes up a lot less space.

Absolutely, that is a great article. Here is the article your link describes, in case anyone wants to read it

Microbiome Dynamics in a Large Artificial Seawater Aquarium

Artificial habitats for animals have high commercial and societal value. Microbial communities (microbiomes) in such habitats may play ecological roles similar to those in nature. However, this hypothesis remains largely untested. Georgia Aquarium's Ocean Voyager (OV) exhibit is a closed-system...

aem.asm.org

That study did show that large water changes disrupt the microbiome. Another recent study confirms that the community is largely stable during routine maintenance.

Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria

Although aquaria are common features of homes and other buildings, little is known about how environmental perturbations (i.e., tank cleaning, water changes, addition of habitat features) impact the diversity and succession of aquarium microbial communities. In this study, we sought to evaluate...

msphere.asm.org

I agree that artificial products can have a large surface area to support microbes, but how to get the right microbes in the first place? Bottled products contain only a handful of types at most, and there is little evidence available that they establish long term populations in the tank. They don't just show up out of nowhere...

 

[AC1211]

I would guess that having a diamond watchman goby would lower diversity in my tank?

 

[AquaBiomics]

Interesting question. Why? Maybe I'm missing something in the question.

I mean, it seems to me sure they stir up the substrate but that should just increase exchange of microbes between water and sediments. (We find lots of surface-associated bacteria in the water already; perhaps your fish might add a few more).

 

[AC1211]

Interesting question. Why? Maybe I'm missing something in the question.

I mean, it seems to me sure they stir up the substrate but that should just increase exchange of microbes between water and sediments. (We find lots of surface-associated bacteria in the water already; perhaps your fish might add a few more).

I thoughr due to their ability to deplete a live sand bed they could lower diversity that was my thinking behind it.

 

[fredk]

I thoughr due to their ability to deplete a live sand bed they could lower diversity that was my thinking behind it.

They would reduce the benthic fauna, the little critters in the sand, but I would not think they would have any impact on bacteria.

 

[Big E]

Absolutely, that is a great article. Here is the article your link describes, in case anyone wants to read it

Microbiome Dynamics in a Large Artificial Seawater Aquarium

Artificial habitats for animals have high commercial and societal value. Microbial communities (microbiomes) in such habitats may play ecological roles similar to those in nature. However, this hypothesis remains largely untested. Georgia Aquarium's Ocean Voyager (OV) exhibit is a closed-system...

aem.asm.org

That study did show that large water changes disrupt the microbiome. Another recent study confirms that the community is largely stable during routine maintenance.

Microbial Community Succession and Nutrient Cycling Responses following Perturbations of Experimental Saltwater Aquaria

Although aquaria are common features of homes and other buildings, little is known about how environmental perturbations (i.e., tank cleaning, water changes, addition of habitat features) impact the diversity and succession of aquarium microbial communities. In this study, we sought to evaluate...

msphere.asm.org

I agree that artificial products can have a large surface area to support microbes, but how to get the right microbes in the first place? Bottled products contain only a handful of types at most, and there is little evidence available that they establish long term populations in the tank. They don't just show up out of nowhere...

Woops, I meant to post two links.......this is the one that has a lot of great info for toay's reefers and answered two questions you posed

Water changes were only a short term change everything balanced back to status quo.
www.advancedaquarist.com/2011/3/aafeature

As far a seeding Siporax I simply set it in my system to be seeded instead of adding hunks of more space eating rock. For my separate frag tank system, I put a piece of rock in a friends system for 3-4 weeks......I never used the bottled products. I had acros & fish in that system the same week I got the rock back. The same can be done with a bag of siporax.

There are some very successful acropora reefs that are fully supported by Siporax only and some light branch rock in the display to mount corals. This allow for better flow, maintenance, ect. in the display.

----------------------------------------------------------------

As far as sand goes I tried it only to get rid of it due to it's issues as a nutrient sink. I could also never keep the surface clean of cyano and other ugly surface algae.

I've kept barebottom systems exclusively for 30 years, because I never saw any useful biological advantages of sand. Just for looks, I tried maybe 3 times and always ended up pulling them.

 

[brandon429]

Not one tank in 30 pages has been harmed by destroying the sandbed in any reef in our sand rinse thread. destroy= either removed totally and instantly without ramp up, tap rinsed, or replaced with all new sand. The bacteria in and on a sandbed are merely extra loading to the system, sand is additional waste catch points, but sand+bacteria do not cause coral decline when ripped right out of place. Upwelling dangerous detritus in some form of mid rot is the risk it’s certainly not the absence of bacteria.

old tank syndrome is caused by accumulation of waste and the bacterial shift associated with accumulation. Old tank syndrome will not occur in a strong throughput system, reef tank bacteria will self balance and self regulate as long as accumulation is prevented, no dosing no refreshing of bacteria no purchases needed.



one of those most important aspects of reef tank microbiology is that we do not have to buy someone’s bottle bac prep to prevent systemic loss, reefs self regulate when you backflush them or pre design them to not catch waste. we have beaten old tank syndrome in a segment of this hobby having never dosed bacteria not once, but merely keeping the systems clean. *our studies are from systems using real live rock at the start, something with coralline on it* not dry systems. Dry systems still get inoculated with diversity with each frag added, each vectoring animal added, but starting with live rock needs to be stated as a core detail at least for the way we measure zero biological lifespan limit for nano reefs.

 

[AquaBiomics]

Woops, I meant to post two links.......this is the one that has a lot of great info for toay's reefers and answered two questions you posed

Water changes were only a short term change everything balanced back to status quo.
www.advancedaquarist.com/2011/3/aafeature

As far a seeding Siporax I simply set it in my system to be seeded instead of adding hunks of more space eating rock. For my separate frag tank system, I put a piece of rock in a friends system for 3-4 weeks......I never used the bottled products. I had acros & fish in that system the same week I got the rock back. The same can be done with a bag of siporax.

There are some very successful acropora reefs that are fully supported by Siporax only and some light branch rock in the display to mount corals. This allow for better flow, maintenance, ect. in the display.

----------------------------------------------------------------

As far as sand goes I tried it only to get rid of it due to it's issues as a nutrient sink. I could also never keep the surface clean of cyano and other ugly surface algae.

I've kept barebottom systems exclusively for 30 years, because I never saw any useful biological advantages of sand. Just for looks, I tried maybe 3 times and always ended up pulling them.

Got it, so you seeded the media by soaking it in an established reef tank for a month or so? Cool. Seems plausible, I havent measured seeding time on fresh media but live rock produces a diverse community throughout the tank in 2 weeks so this seems like a believable time frame.

I like sand too much to give it up. I run frag tanks bare bottom but if I'm looking at the tank I want sand in it. I also struggled with surface algae for a long time but between dosing nitrates and increasing diversity, it appears I've got it beat. Nice white sand in my main DT ever since adding the live sand and mud.

 

[VR28man]

Old tank syndrome will not occur in a strong throughput system, reef tank bacteria will self balance and self regulate as long as accumulation is prevented, no dosing no refreshing of bacteria no purchases needed.

we have beaten old tank syndrome in a segment of this hobby having never dosed bacteria not once, but merely keeping the systems clean.

Interesting. What do you mean by a high throughput system? Are you saying that basically if you flush out your rocks and sand that every so often, you won’t have OTS?

 

[AquaBiomics]

I thoughr due to their ability to deplete a live sand bed they could lower diversity that was my thinking behind it.

Got it. As I understand it they eat micro invertebrates in the sand rather than bacteria. I doubt sand stirrers have any negative effects on sand bed microbes. In a deep sand bed interesting things can happen in hypoxic zones but I think gobies just sift the surface layer mostly.

 

[drawman]

Very nice writeup @AquaBiomics. I'm curious do you take your samples from the display? Certainly would be curious how these communities would change on the rock themselves over time but that's a whole other can of worms.

 

[Rural]

@AquaBiomics
Quick question, if you lived near a swimming ocean beach and your sand pail inadvertantly went home full from wet sand below tide line, would you expect similar results or does the keys have special bacteria properties??? To clarify, would non-reef-area but similar salinity and temparature harvested live sand work?

 

[brandon429]

VR28 yes for sure, and I’m claiming it can be replicated easily. high degree of repeatability such that adherents usually won’t go back to untouched substrate approaches. eliminating detritus and the hordes of competing bacteria it houses, insulates and feeds will absolutely stop old tank syndrome, we don’t even factor the condition as a possibility anymore in today’s nano reef designs. to flush out waste or design for nonstorage restores/preserves surface area from the plugged condition, it oxygenates and reduces waste acid accumulation to be low on detritus storage somehow. The definition of eutrophication is how I define old tank syndrome, sandbed rip cleans force the oligotrophic condition.


We can repeatably install live rock systems that self regulate all bacteria permanently simply by allowing no storage of waste... however that may be attained. it allows for sandbed use and wrasse use etc to know that keeping sandbeds free of impaction in some way is the key to using them safely and long term. I’m for sandbeds, have always had a dsb. Mines just kept clean






part of the problem with previous sandbed science, Berlin, was repeatability. It works for some and then it’s taught as the sole best way based off links to oceanic studies where behaviors chart differently over time vs an aquarium. Now we have to use phosphate adsorption media and nitrate up taking media to offset all the compounding waste. We are now being sold sludge digesting bacteria tabs and bottle bac, to cause this unplugged condition the teachers have had us cause. cyano issues are pronounced in storage style reefs.


tanks absolutely cannot be moved consistently among homes, by web posters, unless a strict prep regimen is implemented which involves ripping out all the accumulation before being set back up. untouched sand beds cause trouble for the masses even if that statement may offend an aquarist who has no trouble keeping one in a large reef at their home. When dealing in raw patterns off work threads, to regulate detritus is to permanently extend the lifespan of a reef aquarium in the condition we expect to see them in. since there are no threads that show how to move reefs place to place keeping the old sand I must infer there to be heavy consequence preventing one from being made. People hate having to rinse all the microbial life out of a tank just to guarantee safe transfer, they would prefer not to disturb the bed if not required for success. detritus locked in various zones of oxygenation= bad and the cause of bacterial imbalance that really matters.