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

[AquaBiomics]

@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?

I havent done the test but here is my speculation. As long as the temp and salinity are similar its likely some of the microbes will survive when you put the sand in your tank. It will surely be a different community from something harvested near a reef but I see no reason to expect that to be a problem.

I think my concern would be other contamination from a swimming beach, including sunscreen which is apparently pretty nasty stuff.

But I'm mostly waving my hands here since I have not measured either bacterial populations or contaminant levels in sand from a swimming beach

 

[Rybren]

My LFS has a few 20+ year old live rock tanks that have 6 inch thick layer of detritus, sediment, and critters in it. Every year or so they give me a cup or two of the sludge and I dump it in the tank.

I don't know whether it helps, but it doesn't seem to hurt anything.

 

[Mark]

I'd like to share an interesting thing I'm experiencing in my reef. I have a mixed reef, with LPS corals that I've grown over a decade alongside a few SPS and a decent diversity of Soft Corals.

For the hell of it, I ordered Florida Keys mud and introduced it into my reef. Since doing so, my stony corals are having tissue die off. It doesn't seem to affect Acros(yet), but Favia/Caulastrea/Fungia/Pavona are all having tissue death. Soft corals are all doing exceptional I realize there could be a multitude of reasons for this. But I have to wonder if that cup of Florida Keys Mud brought in whatever is behind this Stony Coral Disease we are witnessing in the Keys. Far fetched? I don't know. This looks like a bacterial thing, not water chemistry based.

I'm attaching two pics 48 hours apart, I grew this coral from a single polyp over 14 years.. I've lost a Fungia and Herpolitha already. My Caulastrea, which I've kept in various tanks for 16 years is dying as well. While it's depressing to see this happen, the science brain has me genuinely curious as well.

 

[EMeyer]

I'd like to share an interesting thing I'm experiencing in my reef. I have a mixed reef, with LPS corals that I've grown over a decade alongside a few SPS and a decent diversity of Soft Corals.

For the hell of it, I ordered Florida Keys mud and introduced it into my reef. Since doing so, my stony corals are having tissue die off. It doesn't seem to affect Acros(yet), but Favia/Caulastrea/Fungia/Pavona are all having tissue death. Soft corals are all doing exceptional I realize there could be a multitude of reasons for this. But I have to wonder if that cup of Florida Keys Mud brought in whatever is behind this Stony Coral Disease we are witnessing in the Keys. Far fetched? I don't know. This looks like a bacterial thing, not water chemistry based.

I'm attaching two pics 48 hours apart, I grew this coral from a single polyp over 14 years.. I've lost a Fungia and Herpolitha already. My Caulastrea, which I've kept in various tanks for 16 years is dying as well. While it's depressing to see this happen, the science brain has me genuinely curious as well.

I'm both sorry for your coral troubles and curious to know what's in your tank! What you're saying seems plausible to me. Perhaps a batch or collection site effect?

 

[AquaBiomics]

Sorry for any confusion, that post had me so curious I responded from my old account on my phone before checking

Now that I'm on a real keyboard and have had enough coffee I want to add that I didnt find any change in SCTLD-associated bacteria in my tanks after adding the sand and mud, but batch or collection site effects may explain this. If sand and mud can inoculate a tank with beneficial bacteria like NOB I certainly see no reason why they couldnt introduce less desirable bacteria in principle. Interesting...

 

[drawman]

I'd like to share an interesting thing I'm experiencing in my reef. I have a mixed reef, with LPS corals that I've grown over a decade alongside a few SPS and a decent diversity of Soft Corals.

For the hell of it, I ordered Florida Keys mud and introduced it into my reef. Since doing so, my stony corals are having tissue die off. It doesn't seem to affect Acros(yet), but Favia/Caulastrea/Fungia/Pavona are all having tissue death. Soft corals are all doing exceptional I realize there could be a multitude of reasons for this. But I have to wonder if that cup of Florida Keys Mud brought in whatever is behind this Stony Coral Disease we are witnessing in the Keys. Far fetched? I don't know. This looks like a bacterial thing, not water chemistry based.

I'm attaching two pics 48 hours apart, I grew this coral from a single polyp over 14 years.. I've lost a Fungia and Herpolitha already. My Caulastrea, which I've kept in various tanks for 16 years is dying as well. While it's depressing to see this happen, the science brain has me genuinely curious as well.

It may be throwing a dart at the wall but I wonder if a H202 dip would be worthwhile.

 

[Mark]

Sorry for any confusion, that post had me so curious I responded from my old account on my phone before checking

Now that I'm on a real keyboard and have had enough coffee I want to add that I didnt find any change in SCTLD-associated bacteria in my tanks after adding the sand and mud, but batch or collection site effects may explain this. If sand and mud can inoculate a tank with beneficial bacteria like NOB I certainly see no reason why they couldnt introduce less desirable bacteria in principle. Interesting...

Yeah it's interesting. FWIW I ordered the Florida Keys Mud. I do run a UV sterilizer, but I suspect that's not helping with surface bacteria.

It may be throwing a dart at the wall but I wonder if a H202 dip would be worthwhile.

I'm debating a FW dip, which was often used to combat brown jelly. But I'm also curious to find out what's behind it first.

Here's the reference coral this afternoon along with the previous pics:

 

[Fourstars]

I just ordered some keys mud and now you have me worried about introducing to my sump. You have lost more then just this coral? No other changes to your tank or perimeters?

 

[brandon429]

Mark of course I’m slanted to recommend rip cleans, they break too many rules not to be in favor of them.

But isnt one indicated anytime a mass export of a suspect organism is wanted
what other flushing means, safe means, come close to the technique

random bio dosing doesn’t seem as targeted as a move designed to remove everything but the base biofilm left on all surfaces. We can surgically rip full sps systems without harm, we have tricks n sleeves


if suspected microorganisms have been topically introduced into a system then a thorough, flushing reef storm giving no safe harbor in the sandbed + organic insulation any further seems directly indicated over any alternate action, or are my blinders on

act before they reproduce

dipping coral hits the central locus suspected, what about the tank that houses and feeds the organism set, rip them out?

the question isn’t whether we can do large rip cleans successfully, it’s whether a better way exists to clear the environment right at the point you decide the corals are infected.

can wait, if not certain yet but the point of a rip beyond actual mass export is to make way for renewed tank feeding, by not compounding new feed on old waste. It’s beneficial in more ways than one, we show. The tank needs in/out feeding action to put mass back + organic flushing, thats my call because neither are harmful even if the mud never was the problem.

most will never do a rip clean, they’d sooner lose the entire tank this is understood. Even if leaving all organic stores in place is required (housing, feed and insulation for suspects) then at least more target feeding to those corals above norm, plus water changes stepped up to allow for the increase, seems second best move

just so the offer doesn’t sound crazy:

120 gallon rip clean

I’ve decided to perform a rip clean on my 120 with 100% new water. The tank has been running for 5 years and was battling Dino for several months. I used the bacteria method from elegant corals and worked great I haven’t seen Dino in months now. But I tried several other methods including...

www.reef2reef.com

*we could measure your biome afterwards and compare to Jons. You could keep a sample set taken before the cleaning for measures too, keeping in line with the thread title.

 

[Mark]

I just ordered some keys mud and now you have me worried about introducing to my sump. You have lost more then just this coral? No other changes to your tank or perimeters?

Current losses:

• I lost a Fungia that I grew from an Anthocauli(sp?)
• I lost an orange herpolitha that was given to me by a friend that operates a coral farm in Bali. Ironically, the 2nd orange Herpolita is fine.

Currently losing tissue(all 3 of these corals were acquired in 2004 I think):

• The Favia I posted pics of
• The Caulastrea colonies
• My 14" Pavona colony grown from frag

I would add that the mud is very silty and made the tank quite cloudy. Perhaps some silt landed on the corals and created the opportunity for the bacteria to colonize tissue. If you do decide to add it. I would advise rinsing it in a bucket with some old tank water, and then add the larger non-silty grains.

BTW, I don't fault the vendor or anyone. Maybe there is something else going on with the tank. I did combat some dino's last month by restarting my UV and I did run some cuprisorb for a few days(I was worried about iron fueling dinos). But that was weeks ago. The tissue loss in the corals started after the mud. I still think that stimulating bacterial diversity is a good idea. Perhaps I just got unlucky.

I do biweekly small water changes with Tropic Marin. I feed a variety of foods. My current DKH is 9 as usual. PH and Salinity are spot on.

 

[Dan_P]

[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.

Live sand and mud is a complex mixture. What was the diversity of the live sand and mud? Could you have predicted the system’s change in biodiversity knowing what was added in the live sand?

The make up of the bacterial population changed in your systems, but was it a result of adding bacteria, the complex organic matter that stimulate growth of the families that were already present, or both? Is it possible to look for correlations between the size of the change in bacterial family population size and the presence and size of preexisting families? I have to wonder whether you added bacteria or stimulated a shift in preexisting families by the organic matter in the live sand.

Might it be possible to repeat this experiment on a friends’ aquarium using sterilized live sand and mud? Does the diversity change in a similar fashion?

Another important experiment would be to measure the bacteria diversity in the live sand to determine if the size of the change in the system’s biodiversity reflects what was in the live sand or did something in the live sand kill off an important competitor in the system, thus shifting the biodiversity.

Another, very, very important piece of information is whether this shift in biodiversity is repeatable or was this a one time event?

You certainly deserve “I just went down a rabbit hole” t-shirt.

 

[AquaBiomics]

Current losses:

• I lost a Fungia that I grew from an Anthocauli(sp?)
• I lost an orange herpolitha that was given to me by a friend that operates a coral farm in Bali. Ironically, the 2nd orange Herpolita is fine.

Currently losing tissue(all 3 of these corals were acquired in 2004 I think):

• The Favia I posted pics of
• The Caulastrea colonies
• My 14" Pavona colony grown from frag

I would add that the mud is very silty and made the tank quite cloudy. Perhaps some silt landed on the corals and created the opportunity for the bacteria to colonize tissue. If you do decide to add it. I would advise rinsing it in a bucket with some old tank water, and then add the larger non-silty grains.

BTW, I don't fault the vendor or anyone. Maybe there is something else going on with the tank. I did combat some dino's last month by restarting my UV and I did run some cuprisorb for a few days(I was worried about iron fueling dinos). But that was weeks ago. The tissue loss in the corals started after the mud. I still think that stimulating bacterial diversity is a good idea. Perhaps I just got unlucky.

I do biweekly small water changes with Tropic Marin. I feed a variety of foods. My current DKH is 9 as usual. PH and Salinity are spot on.

Interesting. I will say that when I added it to my tanks, I added it in a low flow area of the sump and while it did make the tank cloudy, I didnt see any silt landing on surfaces. It seemed to me the fine stuff got skimmed out overnight in my case.

Occasionally people have expressed skepticism about the value of diversity and I think your case may illustrate their point well -- if a batch of mud (or anything else added to a tank) contains pathogens*, it may harm the tank while increasing diversity.

These are complex experiments we are running in our living rooms! I'll be curious to see what we find in your tank.

[*I feel compelled anytime I use this word to say that the identity of many or most coral pathogens remains unproven]

 

[AquaBiomics]

Live sand and mud is a complex mixture. What was the diversity of the live sand and mud? Could you have predicted the system’s change in biodiversity knowing what was added in the live sand?

The make up of the bacterial population changed in your systems, but was it a result of adding bacteria, the complex organic matter that stimulate growth of the families that were already present, or both? Is it possible to look for correlations between the size of the change in bacterial family population size and the presence and size of preexisting families? I have to wonder whether you added bacteria or stimulated a shift in preexisting families by the organic matter in the live sand.

Might it be possible to repeat this experiment on a friends’ aquarium using sterilized live sand and mud? Does the diversity change in a similar fashion?

Another important experiment would be to measure the bacteria diversity in the live sand to determine if the size of the change in the system’s biodiversity reflects what was in the live sand or did something in the live sand kill off an important competitor in the system, thus shifting the biodiversity.

Another, very, very important piece of information is whether this shift in biodiversity is repeatable or was this a one time event?

You certainly deserve “I just went down a rabbit hole” t-shirt.

As always you raise great questions that are not easy to answer!

I like the questions about nutrients vs inoculation, especially, because these do seem quite testable. Sterilized sand and mud vs non-sterilized. I fear I've become very backlogged with experiments but that absolutely deserves a place on the list. Its testable in a short time frame.

I've wondered whether some of the unknown bottled bacterial mixtures werent getting most of their effects from nutrients rather than live bacteria. It seems fair to ask the same thing about these natural materials...

I will add that many of the changes were qualitative (bacteria absent before adding the mud were present after adding it). But that could just be an issue of the limit of detection, and could still be explained by nutrient effects even if it looks like an inoculation effect.

As far as reproducibility of the effects. I will say that the effects on my two tanks were pretty similar, but not identical (they differed mainly in the response of Flavobacteriaceae). But that only addresses part of the question -- would we see the same effect if someone else did the same thing, a week later?

Could I have predicted the changes ahead of time, based on knowledge of what was in the live sand? In hindsight I'm kicking myself. Great question, I should have sampled the sand and mud themselves! I'll definitely have to include that when I repeat the test.

 

[Dan_P]

As always you raise great questions that are not easy to answer!

I like the questions about nutrients vs inoculation, especially, because these do seem quite testable. Sterilized sand and mud vs non-sterilized. I fear I've become very backlogged with experiments but that absolutely deserves a place on the list. Its testable in a short time frame.

I've wondered whether some of the unknown bottled bacterial mixtures werent getting most of their effects from nutrients rather than live bacteria. It seems fair to ask the same thing about these natural materials...

I will add that many of the changes were qualitative (bacteria absent before adding the mud were present after adding it). But that could just be an issue of the limit of detection, and could still be explained by nutrient effects even if it looks like an inoculation effect.

As far as reproducibility of the effects. I will say that the effects on my two tanks were pretty similar, but not identical (they differed mainly in the response of Flavobacteriaceae). But that only addresses part of the question -- would we see the same effect if someone else did the same thing, a week later?

Could I have predicted the changes ahead of time, based on knowledge of what was in the live sand? In hindsight I'm kicking myself. Great question, I should have sampled the sand and mud themselves! I'll definitely have to include that when I repeat the test.

As always, grateful for the knowledge you are giving us!

 

[drawman]

@Mark I'm curious did your coral dieoff stop?

 

[Mark]

@Mark I'm curious did your coral dieoff stop?

It did. The bacteria or whatever attacking the large Favia did finish the job on that coral. But no other corals were impacted after. I did gather samples for AquaBiomics. But that was right before corona lockdown, and I'm going to guess that access to the lab is not feasible at the moment. No worries on that front, staying healthy is more important. As the disease progressed on the favia, it started to resemble brown jelly disease.

Once the favia die off completed, I did several large water changes. The tank is doing relatively good. I did have a little Cyano on the substrate, but it's almost gone. I think the extra attention with me WFH certainly helped. It's a mixed reef, not exactly full of hard to keep corals. Please forgive the coralline on the back and sides.

 

[Fourstars]

I added Flordia pets sand and mud three weeks ago. Everything doing great and no more Dinos. I did put the sand and mud in a Tupperware with lid to lower, remove top and bury In sump which has a sand bed.

 

[drawman]

It did. The bacteria or whatever attacking the large Favia did finish the job on that coral. But no other corals were impacted after. I did gather samples for AquaBiomics. But that was right before corona lockdown, and I'm going to guess that access to the lab is not feasible at the moment. No worries on that front, staying healthy is more important. As the disease progressed on the favia, it started to resemble brown jelly disease.

Once the favia die off completed, I did several large water changes. The tank is doing relatively good. I did have a little Cyano on the substrate, but it's almost gone. I think the extra attention with me WFH certainly helped. It's a mixed reef, not exactly full of hard to keep corals. Please forgive the coralline on the back and sides.

Glad to hear it! Sucks to lose such a nice coral but glad to hear things rebounded! Tank overall looks great!

I added Flordia pets sand and mud three weeks ago. Everything doing great and no more Dinos. I did put the sand and mud in a Tupperware with lid to lower, remove top and bury In sump which has a sand bed.

This is exactly what I'm hoping to do once they're back in stock. Thanks for the input!

 

[Fourstars]

If you can’t get live sand refresh with some live rock, a bit expensive and got to drive to the airport.

 

[drawman]

If you can’t get live sand refresh with some live rock, a bit expensive and got to drive to the airport.

Yeah hopefully they can get some more in stock. My plan will be to try to load up my sump with dry rock and add the sand and mud as well. I have a ton of sponges and micro feather dusters growing in the sump so it should be hard for the rock to colonize. Just want the the diversity of bacteria!