Cleaning substrate

[JackGulley]

I am sorry, but you guys are not understanding the process. So let's try this.

If you read what Dr. Hovanec writes you will see that he considers having substrate in a new tank being cycled matters as the bacteria colonize it to the extent there is sufficient oxygen. Dr. H. instructs folks doing a cycle to be sure you have some form of substrate on the the bottom of a tank. Here is exactly what he says here
https://www.drtimsaquatics.com/resources/library/quick-guide-to-fishless-cycling-with-one-and-only/



Now, you may want to argue with me, but arguing with the scientist who identified a lot of the bacteria in tanks and has his information published in peer reviewed journals, you will lose the argument every time.

I have done a lot ofcycling and I have used Dr, Tim's One and Only a number of times over the years. (I have never used Safe Start). If you have used One and Only you should have learned a few things. The first is we are instructed to shake the bottle before adding the contents to a tank. The rreason is simple. The bacteria are microscopic and need to be attached to solid particles. These particles are very tiny. And they will sink to the bottom of the bottle and dhaking gets them back into solution. You can clearly see that they are there because you see a white cloud in the water which dissipates as it spreads out to all the places in a tank it will end up. This is the particulate matter to which he bacteria is attached.

But before going one it is important to understand something that becomes easily confusing and that is the term substrate. For the purpose of thos thread substrate refers to the gravel or sand etc. on the bottom of out tanks. But there are two more use of the term as well which are relelvant. The particle to which the bacteria attach are als called substrate and in this case has a different meaning. A piece of gravel or a grain of sand are things we see with out baked eye. But what comes out of bottled bacteria or the sludge we rinse from out filter media or suck out of whatever we have on the bottom of a tank is also called substrate. There is clearly a differenece netween some we can see v.s. something we ned a microscope to view.

The above two uses of the term substrate are not difficult to undestand. The problem is in the third use of the term substrtae in connection with the bacteria or Archaea that actually convert ammonia and nitrite. The ammonia and nitrite are also called substrate. But in this case it refers to what the bacteria use. And the use of the term substrate here refers to what concentration of ammonia or nitrite a specific strain of bacteria need to thrive. And this is what actually determine which starin we have in our tanks.

The term most often seen is substrate affinity. This refers not to particles but to the concentration of ammonia/nitrite on which any given strain can thrive. The term used is substrate affinity. Basically, what is being measured is how much ammonia or nitrite a given strain of bacteria or Archaea needs to thrive. The higher the affinitity, the lower the concentration needed is. So a good example here is the difference between Nitrobacter and Nitrospira. The first thrives in waste water treatment while the second thrives in our aquarums. The nitrospira have a higher affinity which means they thrive at lower concentrations.

So what we have to grasp is that the term substrate has 3 different meanings depending upon the context in which the term is being used. And this will circle us back to the brown sludge we see coming out when we rinse out our filter media or we vacuum the substrate on the bottom of our tank (unless we go bare bottom). This is the bacteria attached to particles. This brown sludge may also be called slime. So let us consider what Dr. Stephan Tanner tells up on this subject.

I would urge everyone to read this article on the Swiss Tropical site: Aquarium Biofiltration . I understand that Dr. Tanner sells Poret foam (among other things, and this is a business which make money for him. But it is also important to know that he is a cancer researcher by profession. He makes money selling Poret. So please put the economic side of things aside for a moment and coinsider the science he explains in terms of using the Poret foam as one's biomedia.



Also,



I know the above is the case as I use Mattenfilters. The water in these tanks is the clearest I have. I do not even consider nitrate in those tanks as I have had the mattenfilters going for years. I know I have denitrification established.

Btw, I have the research papers bookmarked that explain how chloramine doesn't kill the bacteria but puts them to "sleep." The presence of ammonia then wakes them back up. Chlorine can kill the bacteria ina biofilm. But the bio-film protects the bacteria etc. to some extent. research shows that it takes chlorine about 24 hours to penetrate a biofilm completely. The amount of chlorine in our tap water is not great. Smaller concentration of chlorine do not last long enough to do serious damage. It takes a higher concentration of it to wipe out the bacteria.

Lee WH, Wahman DG, Bishop PL, Pressman JG. Free chlorine and monochloramine application to nitrifying biofilm: comparison of biofilm penetration, activity, and viability. Environ Sci Technol. 2011 Feb 15;45(4):1412-9. doi: 10.1021/es1035305. Epub 2011 Jan 12. PMID: 21226531.

Abstract​

Biofilm in drinking water systems is undesirable. Free chlorine and monochloramine are commonly used as secondary drinking water disinfectants, but monochloramine is perceived to penetrate biofilm better than free chlorine. However, this hypothesis remains unconfirmed by direct biofilm monochloramine measurement. This study compared free chlorine and monochloramine biofilm penetration into an undefined mixed-culture nitrifying biofilm by use of microelectrodes and assessed the subsequent effect on biofilm activity and viability by use of dissolved oxygen (DO) microelectrodes and confocal laser scanning microscopy (CLSM) with LIVE/DEAD BacLight. For equivalent chlorine concentrations, monochloramine initially penetrated biofilm 170 times faster than free chlorine, and even after subsequent application to a monochloramine penetrated biofilm, free chlorine penetration was limited. DO profiles paralleled monochloramine profiles, providing evidence that either the biofilm was inactivated with monochloramine's penetration or its persistence reduced available substrate (free ammonia). While this research clearly demonstrated monochloramine's greater penetration, this penetration did not necessarily translate to immediate viability loss. Even though free chlorine's penetration was limited compared to that of monochloramine, it more effectively (on a cell membrane integrity basis) inactivated microorganisms near the biofilm surface. Limited free chlorine penetration has implications when converting to free chlorine in full-scale chloraminated systems in response to nitrification episodes.

Similar articles​

Effect of free ammonia concentration on monochloramine penetration within a nitrifying biofilm and its effect on activity, viability, and recovery.
Pressman JG, Lee WH, Bishop PL, Wahman DG. Water Res. 2012 Mar 1;46(3):882-94. doi: 10.1016/j.watres.2011.11.071. Epub 2011 Dec 7. PMID: 22192761

Three-Dimensional Free Chlorine and Monochloramine Biofilm Penetration: Correlating Penetration with Biofilm Activity and Viability. Lee WH, Pressman JG, Wahman DG. Environ Sci Technol. 2018 Feb 20;52(4):1889-1898. doi: 10.1021/acs.est.7b05215. Epub 2018 Feb 8. PMID: 29376332 Free PMC article.

So, when we clean our media too often or clean too much of the substrate on the bottom of a tank too thoroughly, we may be doing more harm than good. Any of the gunk down in the substrate began as stuff on the surface of that substrte. If we remove some of the gunk on the surface of the substrate, it means there will be less of it breaking down and going deeper.

But, we also know that that when we clean reasonably, that we will not degrade our bio-filtration to the extanet it will create ammonia or nitrite issues. So the trick here is not to over due the cleaning of out substrate and media.

I never vacuum the substrate in my planted tanks unless I am removing a pile of uneaten food. ANd I have some planted tanks for many years that have never been vacuumed. I will conclude this here with one last bit of information. There are some plants in our tanks that actually encourage nitrifying babteria to be ablle to colomize what is usually an aqnaerobic part of a somewhat deep substrtae. The plans will transport oxygen down to their roots where they release it. This creates and aerobic zone in the middle of an anaerobic substarte. The result is nitrification.

Petersen, N.R. and Jensen, K., 1997. Nitrification and denitrification in the rhizosphere of the aquatic macrophyte Lobelia dortmanna L. Limnology and Oceanography, 42(3), pp.529-537.

Abstract​

Nitrogen and O2 transformations were studied in sediments covered by Lobelia dortmanna L.; a combination of 15N isotope pairing and microsensor (O2, NO3−, and NH4+) techniques were used. Transformation rates and microprofiles were compared with data obtained in bare sediments. The two types of sediment were incubated in doublecompartment chambers connected to a continuous flow-through system.

The presence of L. dortmanna profoundly influenced both the nitrification-denitrification activity and porewater profiles of O2, NO3−, and NH4+ within the sediment. The rate of coupled nitrification-denitrification was greater than sixfold higher in L. dortmnanna-vegetated sediment than in bare sediment throughout the light–dark cycle. Illumination of the Lobelia sediment reduced denitrification activity by ∼30%. In contrast, this process was unaffected by light–dark shifts in the bare sediment. Oxygen microprofiles showed that O2 was released from the L. dortmanna roots to the surrounding sediment both during illumination and in darkness. This release of O2 expanded the oxic sediment volume and stimulated nitrification, shown by the high concentrations of NO3− (∼30 µM) that accumulated within the rhizosphere. Both 15N2 isotope and microsensor data showed that the root-associated nitrification site was surrounded by two sites of denitrification above and below, and this led to a more efficient coupling between nitrification and denitrification in the Lobelia sediment than in the bare sediment.
from https://aslopubs.onlinelibrary.wiley.com/doi/epdf/10.4319/lo.1997.42.3.0529

?
No one’s talking about having a bare-bottom tank. OP was asking how deep into the substrate you should stick the gravel vac.

 

[Endlersendlers]

Imagine your tank as a city. The filter media is like a large town city center designed for beneficial bacteria.

The substrate and decorations are like suburban neighborhoods with plenty of space for these microbes to dwell. The entire tank, with all its nooks and crannies, represents the whole town where the beneficial bacteria population is spread out.

There is always a higher concentration of peoples in the city center than the suburbs. But the suburbs are generally much larger.

Depending on the setup: Light, plants, coarseness of the substrate, water circulation. The ratio between the one living in the center and the suburban area can vary a lot.

There is also another factor: Frequency, the more often you vacuum the substrate the less bacteria you remove. Because they are attached to solid surface of the substrate instead of detritus that are removed at this point.

By doing it regularly and preventing mulm to clog the substrate you are keeping the best conditions possible.

Terrific analogy!

 

[Endlersendlers]

In plain English, I vacuum gravel to the glass and swirl just over sand to get detritus on the surface. Things fall in between the gravel and get to the bottom. Some stuff they sell as sand is large like small gravel and not like beach sand. I vacuum that to the glass bottom. If it is fine sand, stuff doesn’t fall in between but sits on the surface where swirling the vacuum hose above it loosens it and vacuum it off. You should still stir up the sand a little now and then to prevent anaerobic (no oxygen) pockets from building up and growing bad bacteria. If you don’t do this, the bacteria that grows in anaerobic pockets can build up and make toxic gases, and one day that bubble releases and kills some fish and you would never know why.

I don’t agree with never cleaning the gravel or sand substrate and only doing water changes. Gravel will create anaerobic pockets too if enough muck builds up in it, then poisons the fish when that pocket releases. Bad (anaerobic) bacteria build up that can cause disease when muck builds up so that oxygen isn’t getting into these areas. Whoever insists you only need to do huge water changes twice a week because it all dissolves in the water doesn’t realize how much extra work they are creating for themselves and, until they gravel clean one day and see what they get out, won’t realize it’s accumulating at the bottom. A small, small percentage dissolves and is removed with those water changes. The longer between gravel vacuums, the more there is. That proves it’s not all dissolving in the water you’re changing.

 

[Endlersendlers]

Beneficial bacteria grows in places oxygen can get to. That’s another reason for vacuuming the gravel. It stirs up the gravel as well as removing muck so you don’t have unoxygenated areas that grow gram negative (bad) bacteria. Enough bacteria sticks to the sand or gravel to keep the cycle going. Stirring it up is to make sure the oxygenated water gets in there enough to prevent the bad bacteria from growing. It doesn’t take much. If the tank gets cloudy as you’re doing it, it’s time to reevaluate your technique to be slower and more careful or move the vacuum such that it gets the whole plume as lifting slowly before moving to another area, or maybe it’s been too long since it was last done and you need to stop and do a section at a time not to harm the fish or invertebrates with all that in their water. Hope that helps!

 

[jaylach]

Beneficial bacteria grows in places oxygen can get to. That’s another reason for vacuuming the gravel. It stirs up the gravel as well as removing muck so you don’t have unoxygenated areas that grow gram negative (bad) bacteria. Enough bacteria sticks to the sand or gravel to keep the cycle going. Stirring it up is to make sure the oxygenated water gets in there enough to prevent the bad bacteria from growing. It doesn’t take much. If the tank gets cloudy as you’re doing it, it’s time to reevaluate your technique to be slower and more careful or move the vacuum such that it gets the whole plume as lifting slowly before moving to another area, or maybe it’s been too long since it was last done and you need to stop and do a section at a time not to harm the fish or invertebrates with all that in their water. Hope that helps!

Oxygen for bacteria is one of the reasons I like under gravel filtration as oxygenated water is constant,y being put through the entire substrate.

 

[FishyD]

It depends is probably my answer. I hover over the substrate, (gravel in my case) over Fluval Stratum in my heavily planted tanks. As long as there is no excessive mulm or any other debris I stick to this plan and parameters and plants remain happy. They tend to take care of themselves so I don;t disturb them on a regular basis. Every few months I might vacuum a little deeper just to monitor if things are staying normal. If I kept fish that created a lot more waste, I would probably vacuum a little deeper. Hospital tanks are bare bottom, QT tanks thin layer of substrate so it's easy to deep clean after the current batch rotates out to main tanks.

 

[FishyD]

I gravel clean but, for me, it is needed as I run under gravel filtration and doing a vacuum of the gravel helps to prevent a buildup of crud under the filter plates. I also leave the area around planted plants alone.

I don't want to highjack a thread, but I haven't run an under gravel since the 80's. It seemed like it didn't work too bad, but I am sure things have changed since then to say the least. Is there a place where I might read about modern techniques for a UG filter?

 

[jaylach]

I don't want to highjack a thread, but I haven't run an under gravel since the 80's. It seemed like it didn't work too bad, but I am sure things have changed since then to say the least. Is there a place where I might read about modern techniques for a UG filter?

There is no difference between UG now and the 80's. Bottom plates, gravel and air risers with air stones or power heads.

 

[Oldspartan]

I keep it simple. Every third wc (12 days) I vac the top. Every 6th wc (24) days I move things around and vac to the bottom.

No science or lengthy experience behind the method. Just feels right, my water is stable, and no mortality. Even the fry avoid mortality.

I like having a system. Really I need a system.

 

[Fishfunn]

All the diseases that befell my tanks over the years always happened when I didnt clean the gravel. Waste in the substrate is a breeding ground for bacteria and dreaded parasites. Whenever I do a water change, I vacuum from the top to the bottom. Not only does the gravel look better, but my fish are very healthy and happy.
Besides I look at it this way, if I had waste in my living space, I rather have it gone then having to smell and taste it! Fish are no different.

 

[TwoTankAmin]

And I get the exact opposite results as FishFunn reports above. As I wrote earlier in this thread, I never vacuum my planted tanks. When I kept my high tech panted tank with pressurized co2 and high light levels for close to a decade, it was without question the healthiest tank I have kept. In the 9+ years it ran, I had only a single death in the tank (I lost one of the 3 farlowellas I added to it after about 6 or 7 years). I never needed to medicate this tank the whole time I had it.

The substrate depth was between 3 and 4 inches throughout. Early on I did vacuum the plants when they got "dirty." That was because fine particles would sometimes settle on the plant leaves or get into the dwarf hairgrass and I would vacuum the plants but not the gravel. This was not a very frequent occurrence. It took me a bit of time to get things balanced. I also had a couple a beds of baby tears which would become so dense after a few months that the leaf mass would begin to rise and that exposed the lower shaded portion not have leaves. This looked awful. The replsnting stirred up the substrate some and when things settles I had to vac., the plants

The result was that about every 3 - 4 months I would remove the entire mass of baby tears and replant about 5% of it (the rest got flushed). This process caused some of the gunk in the substrate to get into the water column and, as it settled, some of it would settle on the plants. They got vacuumed, but the substrate never did. I also had to pull up, cut in half and replant the top half of all the stem plants in the tank about every couple of months.

One the other hand, I had a number of species tanks in which I had plecos spawning and I also had tanks for growing out the offspring. None of these was planted and most had a sand substrate with a depth of about an inch. These tanks were pretty heavily stocked and were well fed. All had sand bottoms. So these tanks needed to be vacuumed regularly.

However, these pleco tanks all used massive amounts of Poret foam filtration. Several used Hamburg Matten filters and the rest used multiple Poret Cubefilters 4x4x4 and 5x5x5 inches- all were 20 ppi porosity. These compensated for the weekly vacuuming I had to do which was a mix of surface vacuuming and down to the bottom class vacuuming. The vacuuming tended to change which sand was on top and which was on the bottom depthwise. If the sand closer to the surface got moved to the bottom, the bacteria in it did not fare well. So the massive foam was the primary filter media and where most of the bacteria resided.

So I needed massive media to insure adequate bacterial colonies would persist. On the other hand most of my planted tanks had a deeper substrate. This was at least 2 inches and closer to 3 in many tanks. I also have a 75 gal. tank with barely an inch of sand,It is heavily planted. But there are many abubias and ferns on rocks or wood. In addition I have severl terracotta pots with substrate and these are planted. I never vaccuum this tank.

If a lot of substrate which was never vacuumed was toxic to fish, I should have been killing fish regularly. But it did not happen. Here is the tank with substrate and terracing before it was planted. The gravel was 3 or more inches deep everywhere. The filtration was an Ehiem Pro II 2026 canister.

Over the decade I had it the plants were redone a few times and I changed the fish in the tank as well.

And I also had farlowellas spawn in this tank.

There was really no way to have vacuumed this tank in most of its incarnations.

What I do know is that the best filtration one can have is live plants and a deep substrate that is never vacuumed. And when I do no use plants then I use massive foam filtration which us the next best form of filtration when live plants are not used.

The reason I mentioned bare bottom tanks was because they needed to be vacuumed more often than my tanks with substrate. With no subtrate histing bacteria, having more bio-media was necessary. And the advantage of massive amounts of poret foam, specially as Matten filters but laso the ubefilters provide more than ebough places for the bacteria to colonize in a stable fashion. I cleane the Matten on a schedule of miultiple years not week or months.

 

[WhistlingBadger]

I just suck the mulm off the surface when it starts to look ugly. I figure whatever gets down into the sand, the plants can take care of. My tanks constantly register <5 ppm nitrate and only have parasite problems when I fail to quarantine new fish, so I guess it's working.

 

[WhistlingBadger]

Gravel will create anaerobic pockets too if enough muck builds up in it, then poisons the fish when that pocket releases. Bad (anaerobic) bacteria build up that can cause disease when muck builds up so that oxygen isn’t getting into these areas.

That is true, unless you have plants. Plant roots oxygenate those anaerobic areas and keep them from becoming toxic.

 

[Rxhart]

I have an interesting situation regarding substrate. There are hundreds of snails living and aerating and eating in the substrate. These are the dreaded Malaisian trumpet snails. To keep them in check I remove probably 30 a day and feed to 7 happy puffers . I also have a loach to eat them. Anyway, they seem to keep the substrate healthy and clean, so I don’t vacuum. The 9 adult angels living in the planted tank seem perfectly happy with this arrangement with monthly water changes of 25%. Tank seems perfectly balanced. Sometimes I have to clean off the algae on the glass, but otherwise I have thriving breeding fish and some happy little dithers and a sneaky catfish in there.