Cleaning substrate

[gwand]

I should have asked this question a long time ago. I clean the top 1/2 inch of my substrate with each weekly water exchange. Today in my lfs they were cleaning the substrate until they hit glass on the bottom of the tank. Does anyone do this weekly, monthly, quarterly, not at all etc.

 

[MattW]

Before I kept live plants I gravel vacced and sometimes removed the substrate to the glass bottom entirely in which I cleaned in aquarium water. I did that mainly to remove old rotting flake food that my then danios didn’t eat. Now I don’t do any of that, only water changes. Plants do that work for me along with detritus worms, copepods, etc

 

[Ceez]

I always clean down as far as possible. The water looks like a dust storm or cloudy when I hit the glass so I feel like I'm getting more for my money. I'm already putting it in the substrate why not go all the way.

 

[Colin_T]

I gravel clean down to the glass every time I do a water change.

I don't gravel clean right up to the base of plants. I leave an inch or two of undisturbed substrate around each plant for the plant roots and gravel clean open areas. I also do under rocks and wood to stop anaerobic pockets forming under them.

 

[jaylach]

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.

 

[TwoTankAmin]

It depends on the tank. I do not vacuum my planted tanks at all. The plants love the mulm and I do not remove it.

There is also beneficial bacteria in the top of the substrate. But it is barely as far down as an inch and likely even less. There is not sufficient oxygen at an inch or lower to support the nitrifiers. I am more likely to vacuum beyond just the surface in tanks where I have Hamburg Mattenfilters and/or several Poret foam cubefilters.

It is possible to control where the bacteria will be found in the greatest number by how you clean what, and when. The bacteria will naturally colonize where they can get the most of what they need delivered to them. And what they need is mostly oxygen, inorganic carbon, iron, ammonia and nitrite (and if we are lucky nitrate removal via facultative bacteria. These can use oxygen when it is present and, when it isn't, they can switch to using nitrate and they then create N2 gas. This is the completeion of the nitrogen cycle--> Nitrogen (N) is fixed in ammonia (NH4)--> nitrite (NO2)--> Nitrate (NO3)--> Nitrogen gas (N2 )

Nitrogen always exists as N2 in nature. Actually, it's rare for there to just be a stand-alone element not bonded to something.

Now we know the bacteria is in the filter media, in the top of the substrate, and then on almost any other hard surface which gets decent circulation and which is out of the light. The bacteria are somewhat photophobic. So they will be on the undersides of things or on parts of the plants not well illuminated- (stems, under thick leaves and even the roots in some cases).

One we understand that the bacteria do not move much andthat they need everything delivered to them, there is one more relevant factor to consider. While we know the nitrifiers are slow to reproduce, we also know that under optimal conditions trhe ammonia ones will do so in about 8 hours and the nitrite ones in about 1/2 a day.

Now it comes time to do rgeular maint. and water change etc. If we vacuum the substrate below the surface, we will be removing some of the good bacteria. Similarly, if we rinse out the bio-media where the nitrifiers are attached the same loos will occur. The more things we clean that host the bacteria we want, the more bacteria which can be removed from the tank. However, what we are not doing is removing a great deal of the total bacteria. Doing that reauires a serious effort.

So let's assume what we do is to remove as much as 1/3 of the bacteria. What we know is, in a matter of hours, the bacteria will be back up to full strength. And the odds are that we will never test for ammonia or nitrite. The reason is that the ammonia and nitrite in a tank is being created gradually 24/7. If we could add it all up it would still usually be less than the ammount of ammonia we dose during a fishless cycle.

So now if we just think about all of the above, a light bulb should turn on above our head. If we cleaned only the media in the filter, that is the only place from which we will be removing bacteria. And when we do this, it is all of the remaining bacteria all over the tank that will have more ammonia/nitrite than they need to thrive and this sets them all to multiplying unti their numbers increase to handle all of the ammonia/nitrite.

The net result when this all is done is that the will be less of the total bacteria in the filter media and more of it in other places in the tank that are bacteria friendly. Basically, the colonies in the tank will add up to about the same total amount of bacteria as we had before we did the maint. However, there will be more individuals in other places and fewer in the filter media. This would make it look like the bacteria moved, but they didn't.

Apologies for a slightly long explanation.

So, how we clean a filter and then the rest of a tank, especially the substrate, can alter what the numbers are when we finish and the bacteria reproduce back to the needed numbers for the tank to be safe. fFor most of us, the dechlor we use also detoxifies ammonia. The bacteria can still use it but not as efficientl;y. But the detoxifying basically turn is to ammonium (NH4). This is way less toxic than ammonia (NH3).

When I cycle filters in my bio-farm, I am overloading them with the needed bacteria. My biofarm is bare bottom. But when I move the filters in to their new tanks, the bacteria will start to spread out beyond the filter to some extant. ANd here is a bit of a surprise because, at any time, a small portion of the bacteria are motile. This is one ot their survival strategies. In addition, bits of a biofilms occasionally become detached by current. Where this bit of biofilm with its bacteria lands may be the start off a new colony or it could be in a place they cannot live so they die.

What percent of the bacteria are motile is dependent on the nitrogen content in the water. When normal, the fewest number are motile, but when the amount of needed nitrogen drops, more of the bacteria become motile. At best this is around 10%. SAnd their raison d'etre is to flee hoping to end up where they can get what they need nd thus colonize, before they die while still looking.

In a tank there is no other place to go and their motility is of little use. The main survival strategy for the bacteria when they sense that any of the essential things they need to survive is no longer available, is that they go into state of dormancy. But if some of the normally motile few land and attach someplace new in a tank, all the better. The motile bacteria have one goal, to move. They are not swimming around oxidizing they are looking for a new home/biofilm in which to live.

So, I basically herd my bacteria, it least it looks that way. By having massive bio-media, I know if I vac deeper in the substrate I am encouraging the bacterial numbers in the available massive foam space to multiply. However, In my well planted tanks I have less bacteria in my filter media because the plants host bacteria as does the substrate. But the plants also use more of the tmmonai than the bacteria, Plants out compete the bacteria, but not to the point of making them all disappear.

One can have a well established, cycled tank with no plants,\. But, no matter how many plants, nor what types, one has in a tank, there will always be some amount of nitryfing bacteria present..

 

[MaloK]

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.

 

[10 Tanks]

Hello. I don't vacuum the bottom material. All that organic material is constantly dissolving in the tank water. So, by just performing a large water change, I can remove most of the material that's dissolved.

10

 

[JackGulley]

I understand the arguments against gravel vac-ing on paper, but in my experience it just doesn’t work out in practice. If I don’t vacuum the gravel, it gets full of detritus that pollutes the whole tank every time I try to move the gravel at all. It might be good for the plants, but that doesn’t mean they’ll keep it in check. With gravel substrate I just don’t think anything that’s naturally happening in the tank is going to stir the gravel enough to bring that stuff into the water and then the filter. Maybe it’s different with sand and some digging bottom-feeders, but with gravel, no.

That said regarding the original question, I try to vac all the way to the glass, but I do the areas with plant roots more delicately.

 

[TwoTankAmin]

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/

Tips and Troubleshooting:

• IMPORTANT – Do not let the ammonia OR nitrite concentration get above 5 ppm.
• NOTE – As of November 2016 DrTim’s changed their ammonium chloride solution and you use 4 drops per gallon instead of 1 drop per gallon. Read the label on the bottle you have and follow the directions on the bottle.
• If either ammonia or nitrite concentration get above 5 ppm, do water changes to lower the concentration.
• Do not let the pH drop below 7. If it does, do a partial water change to bring the pH back up.
• Do not add ammonia removers to bind the ammonia – overdosing with these products will just increase the cycling time.
• You do not have to add ammonia everyday – the bacteria do not have to be fed every day. Adding ammonia everyday will results in a sky-high nitrite reading and slow the cycling process.
• Is your tank bare-bottom? – if your tank does not have substrate (gravel or crushed coral) on the bottom this is called a bare-bottom tank and they take longer to cycle because there is not very much substrate for the bacteria to adhere to. If you are setting-up a quarantine tank and do not want to use a traditional substrate consider adding some inert glass rock or marbles or some other non-calcium-based media to the tank bottom. This will help cycle the tank faster.

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.

Q: how do rinse Poret® foam sheets?

A: the easiest way is outside in the yard or driveway using a garden hose. Simply bang the sheet flat on the ground several times (Note: I recommend not wearing your best outfit doing this) to shake out the filter sludge, then rinse with the hose; repeat until the water coming out is relatively clean. Don’t overdo it! Sufficient microorganisms will survive this procedure to quickly re-establish the biology of the filter. It does not matter if you use cold or chlorine-treated water! The often repeated notion that this process would kill all the filter organisms is complete nonsense, because the residual chlorine concentration in drinking water is way too low to kill them.

Also,

All filters break down proteins and ammonium to nitrate and do so mostly based on the amount of food added to the tank. Filters do not make NO2 or NO3 out of thin air. Depending on the surface area filters also denitrify NO3 into elementary N2 with anaerobic microorganism. It is often mentioned that happens only in deep substrate layers or live rock but that is not the complete story. Biofilms that cover any surface in the tank (and most importantly the large inner foam surface) have aerobes residing in the top layers. But in the lower layers they contain anaerobes that use the oxygen in NO3 for their metabolism. The reason why the huge surface area in both Mattenfilters and Cornerfilters works so well is that the material does not clog and thus runs undisturbed for long periods of many months or even years. Hence, the biofilm becomes more mature and then breaks down more NO3. Of course, after many months or even years or with a heavy waste load, the foam like any other media needs to be rinsed to remove excess organic material to work properly.

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

 

[Fishfunn]

I should have asked this question a long time ago. I clean the top 1/2 inch of my substrate with each weekly water exchange. Today in my lfs they were cleaning the substrate until they hit glass on the bottom of the tank. Does anyone do this weekly, monthly, quarterly, not at all etc.

Yes, I do it all the way to the glass to get it clean. I am careful vacuuming up the entire plume of waste so none falls into the water column. I basically use my Python to vacuum the gravel then have the gravel fall back out with no waste or bacteria going into the water column.

So I like to have my gravel no more than 1 to 2 inch thick for cleanliness purposes.

 

[gwand]

Yes, I do it all the way to the glass to get it clean. I am careful vacuuming up the entire plume of waste so none falls into the water column. I basically use my Python to vacuum the gravel then have the gravel fall back out with no waste or bacteria going into the water column.

So I like to have my gravel no more than 1 to 2 inch thick for cleanliness purposes.

The bottom of my tank is black sand. When I use my python to vacuum to the very bottom of the tank, the sand goes through all the way into the sink. Any ideas how I can vacuum to the glass getting the crud but leave the sand behind? Thanks.

 

[gwand]

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

That is a lot of information you offer. Thank you. However, I need the executive summary. Do you vacuum a Sandy substrate all the way to the glass of the tank or do you vacuum just the surface of the substrate picking up poop an uneaten food. is the bacteria contained in the sand all the way down to the glass necessary to maintain a healthy nitrogen cycle?

 

[Fishfunn]

The bottom of my tank is black sand. When I use my python to vacuum to the very bottom of the tank, the sand goes through all the way into the sink. Any ideas how I can vacuum to the glass getting the crud but leave the sand behind? Thanks.

I would try crimping the hose before the sand gets to the of the tube so the sand will fall back down leaving the plume in the tube.

I use the black plant substrate, 'CaribSea Eco-Complete Planted Aquarium Substrate', that is bigger than sand that I like a lot.

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[MaloK]

I vacuum sandy surface with a medium sponge over the tip of a simple tube held with a cable tie, I use my thumb over the output to release sand after doing an area, the mulm goes trough the sponge but not the sand.