Looking after your bacteria :)

[Masha]

The more I learn about it, the more it seems that fish keeping is really bacteria keeping

I found this article (I think it was a link from fishfur? My firewall threw a false positive, calling it "harmful" but when I queried it, it turns out that the page is quite safe) Bacteria in the Freshwater Aquarium

Here is something I found very interesting - quote from the article (bolding is mine):


These species of heterotrophic bacteria break down dead organic matter like fish waste, dead fish or plant matter, uneaten fish food, dead bacteria, etc. Some are aerobic, but many species are facultative anaerobes, able to live with or without oxygen.
...

These bacteria have only one requirement to appear and live: organics. They compete with autotrophic bacteria for both oxygen and surface area; studies show that even in relatively clean environments, they occupy more than 50% of the available surface area. And given that they can reproduce within 15-60 minutes—compare this to the 12-32 hours required by nitrifying bacteria—you can see how easily these heterotrophic bacteria can overwhelm the system. In a filter, if sludge is allowed to increase, heterotrophic bacteria will multiply so fast they actually smother and kill the autotrophic nitrifying bacteria.



And this too:


The greatest population of bacteria in a healthy balanced aquarium occurs in the substrate, not the filter. The floc or humic compost that collects in the substrate is the host for the biofilms; this is why the substrate in planted tanks should never be disturbed, and many aquarists apply this to non-planted tanks as well.

In very general terms, aerobic nitrification takes place in the top 1-2 inches of the substrate; anaerobic de-nitrification takes place approximately 2-4 inches down, and anaerobic bacteria producing hydrogen sulfide occurs in substrates deeper than 3-4 inches. In all three cases, it will be deeper in coarse substrates (like pea gravel) and more shallow in finer substrates such as sand. These generalities will also vary with the presence of live plant roots and substrate “diggers” such as snails and worms, since these factors result in more oxygen being made available in the substrate, reducing anaerobic bacteria activity. An oxygen level in the substrate of as little as 1 ppm promotes nitrogen reduction rather than sulfur reduction (hydrogen sulfide). [6]

Maintaining a substrate of fine gravel or sand no deeper than 4 inches, having live plants rooted in the substrate, and keeping Malaysian Livebearing snails are the best and safest methods of providing a healthy biological system for aerobic and denitrifying anaerobic bacteria.



I did not know that the sludge in your filter could be from heterotrophic bacteria? I always thought that you had to rinse it simply to keep the water-flow going, so the BB gets enough oxygen?

And this also explains why you should be careful of doing gravel vacs? Cleaning the gravel gets rid of the good BB?

Also that heaping up your substrate deeper than 4 inches might be a bad idea?

I really want to get some Malaysian trumpet snails now

 

[Masha]

...also thinking now...trying to start a cycle with scrapings from a filter in an established tank might not work, if that filter has not been well maintained. The sludge would be the wrong kind of bacteria, and the tank might be cycled because of the BB in the substrate - whether or not the owner of the tank is aware of that fact?

 

[Cactuspixie]

Thanks for that link Masha! It was very informative

 

[Wy Renegade]

Good questions and good points. I love discussions about bacteria, so I'm tagging along ~ mainly cause I know that at least one of those points is going to generate a lot of controversy .

 

[jlk]

The greatest population of bacteria in a healthy balanced aquarium occurs in the substrate, not the filter.

If this were true, you would not be able to cycle a bare bottom tank. I, as well as others, have kept successful bare bottom tanks and this includes cleaning the 'biofilm' regularly from the glass (or a bb tank looks rather vile). When I kept gravel in the past, I actually cleaned it daily with a portable vac as well as during water changes with a siphon. Never saw a cycle disruption. I have also switched substrates completely without even the slightest disturbance in a cycle. I place no importance on gravel or any other substrate as the primary source of bacteria so I must disagree completely with this. Heterotrophs exist in abundance and multiply quickly- its the autotrophic (nitrifying) bacteria that you need to keep happy.

 

[Thumper828]

 

[Masha]

If this were true, you would not be able to cycle a bare bottom tank. I, as well as others, have kept successful bare bottom tanks and this includes cleaning the 'biofilm' regularly from the glass (or a bb tank looks rather vile). When I kept gravel in the past, I actually cleaned it daily with a portable vac as well as during water changes with a siphon. Never saw a cycle disruption. I have also switched substrates completely without even the slightest disturbance in a cycle. I place no importance on gravel or any other substrate as the primary source of bacteria so I must disagree completely with this. Heterotrophs exist in abundance and multiply quickly- its the autotrophic (nitrifying) bacteria that you need to keep happy.

Apparently I've accidentally stumbled onto something controversial

JLK I'm obviously a complete beginner so I don't have an opinion on this myself -- just trying to learn

Is it possible that the statement from the article does not mean that a bare bottom tank has no nitrifying bacteria, (which is clearly not the case, as you say) but that in a bare bottom tank, the majority of the nitrifying bacteria would be in the filter? Since it has to be somewhere, and there is no substrate to colonise?

Could a bare bottom tank's filter have a larger colony of bacteria than the equivalent tank with substrate?

One of the reasons I find this interesting is because of this:

I just moved my fish from a smaller tank to a larger one. I plan to possibly use the smaller tank as my quarantine tank. Being ignorant, I had allowed the filters in the small tank to get rather clogged up. There's still some flow through but not much. The tank was cycled - water parameters were fine.

I thought I would be clever and cleaned the gravel very thoroughly. Seemed like the right thing to do. Of course, now the tank is no longer cycled. Seems that in this case -- with suboptimal filtration -- most of the BB was in the substrate and I've got to start cycling this tank again from scratch. Luckily there are no fish in there.

(I'm still deciding whether this will be a permanent quarantine tank, or whether to set it up with a betta, which is why I did not simply take out all the gravel. Quarantine tank is better without gravel, am I right?)

 

[severum mama]

How do you know that the tank was no longer cycled, given that it was no longer housing a fish load after you switched tanks?

 

[Masha]

How do you know that the tank was no longer cycled, given that it was no longer housing a fish load after you switched tanks?

I added a small amount of ammonia and tested after 24 hours --it was still all there. Previously, with my fish in there there was no ammonia. So I guess that I've broken my cycle?

 

[Masha]

Well, that's interesting.

I just tested that tank again - seems like the BB has been doing a lot of catching up.

My results were like this:
Cleaned the gravel and filters.
Dosed with 1.25 ammonia. 24 hours later, ammonia still at 1.25
Did not test anything else.

Tested again 36 hours later - ammonia 0, nitrite 0, nitrate 12.5

So it looks like I did not completely destroy the BB by cleaning the gravel so thoroughly, although I definitely harmed it. I'm hoping that cleaning the filters had helped though, as now the BB can grow in there. Going to add a higher dose of ammonia now and see whether maybe this tank is close to cycled already?

 

[PerfectDepth]

So it looks like I did not completely destroy the BB by cleaning the gravel so thoroughly, although I definitely harmed it. I'm hoping that cleaning the filters had helped though, as now the BB can grow in there. Going to add a higher dose of ammonia now and see whether maybe this tank is close to cycled already?

Did you clean out your filter and thoroughly vacuum the gravel at the same time? That might be why you had a mini-cycle. If you would have waited a week or two in between you probably wouldn't have had a problem.

The greatest population of bacteria in a healthy balanced aquarium occurs in the substrate, not the filter.

It was once explained to me that the bacteria mainly inhabit any surface where there is more water flow. From this I gather that the percentage of bb in the substrate will depend on your setup, and the amount of water current near the bottom.

To me, it makes more sense that the majority of the bacteria inhabiting the substrate is the exception, not the rule. Otherwise, we would be better off placing our bio-media at the bottom of the tank instead of inside the filter, right?

Good topic! My tank is only 10 gallons, so it's important for me to keep the bio-filter healthy to avoid problems. I'm always trying to learn more about it.

 

[jlk]

It just sounds like you did too much at once and it disrupted your tank's balance. You did not destroy your cycle and your bacteria should be back up to speed in a few days to maybe a week at most. Keep the ammonia dose low for now until they get back up to speed then gradually increase it over a couple of days so you don't overwhelm them with a big dose of ammonia. Then just stick to a regular maintenance schedule to keep everything running smoothly. Alternating cleaning filter media (one piece one week something else the following week or in two weeks) and gravel vac'ing sections of a tank at time will help!

 

[Wy Renegade]

If this were true, you would not be able to cycle a bare bottom tank. I, as well as others, have kept successful bare bottom tanks and this includes cleaning the 'biofilm' regularly from the glass (or a bb tank looks rather vile). When I kept gravel in the past, I actually cleaned it daily with a portable vac as well as during water changes with a siphon. Never saw a cycle disruption. I have also switched substrates completely without even the slightest disturbance in a cycle. I place no importance on gravel or any other substrate as the primary source of bacteria so I must disagree completely with this. Heterotrophs exist in abundance and multiply quickly- its the autotrophic (nitrifying) bacteria that you need to keep happy.

One does not necessarily imply the other. As Masha pointed out, the research the author is referencing obviously was conducted in a tank with substrate. The fact remains that people ran aquariums successfully for years (and some still do) using undergravel filters where the only possible location for the bacteria was the substrate. I'm often confused by why people are so willing to dismiss the likelyhood of a thriving population of bacteria in the substrate, as it seems to me, if an individual were to maintain both, they in the event of a mechanical or electrical shut-down, they can still be confident in the filter capability of their system.

Is it possible that the statement from the article does not mean that a bare bottom tank has no nitrifying bacteria, (which is clearly not the case, as you say) but that in a bare bottom tank, the majority of the nitrifying bacteria would be in the filter? Since it has to be somewhere, and there is no substrate to colonise?

Could a bare bottom tank's filter have a larger colony of bacteria than the equivalent tank with substrate?

Absolutely! The reason the topic is controversial is because it is generally believed that modern medias present in today's filters actually contain more surface area than the substrate in our aquariums. Hence the largest population of bacteria would be present in the filter rather than on the substrate. Regardless of where that "largest" population occurs, the fact remains that bacteria will colonize every surface in your aquarium, so it is quite possible to have a large healthy population of bacteria in your substrate. Once again however, this depends on the surface area present in the substrate for aerobic bacteria. With many people switching to a sand-based substrate, the available surface area becomes very minimal. Recent research has show that even a relatively thin layer of sand (1/4" in depth), has the potential to house sulfide releasing anaerobic bacteria. I've often wondered why we so seldom hear anything about this risk in freshwater tanks. Perhaps it is because those with sand substrate don't disturb their substrate much? The presence of bacteria in the substrate is the basis behind those who argue that with the right set-up, it is possible to maintain an aquarium without any filter system. Now that is a controversial topic . It would be really interesting to spending some time looking at the authors research as well as dates the research was conducted in order to get a basis for that conclusion.

 

[Masha]

Thanks for all the thought provoking answers, everyone.

 

[Paul1792]

Gravel vacuums simply do not cause loss of bb

Think about it. BB attaches to gravel in the same manner as it attaches to the bio-media in your filter. If water rushing through an HOB filter at 300 gallons per hour doesn't wash BB off the little "bio-rocks" (ie seachem matrix or equivalent) in an AquaClear 70, the BB sure isn't going to be "washed off" the gravel with the speed of water flowing into a siphon.

Gravel vacuums are important to remove fish droppings and uneaten food which turn to ammonia ->nitrites->nitrates. Unless you plants are taking care of all the "junk" on the bottom of the aquarium, you'd better be doing massive water changes.

Since I must use $1/gallon spring water due to poor local water supply, I do 25% water changes only twice a month along with thorough vacuums of the substrate (I use fake plants) and despite the over-stocking in my 38 gallon, my readings stay:

ammonia: 0
nitrite: 0
nitrate: 5-10.

I was only aiming for nitrates at under 30 ppm so I/m very happy with the way it's working. Water is crystal clear and polished, no odor, no loss of fish. Fish are vibrant, happy & healthy.

Watch 'em in action here:

38 Gallon Community Video by Paul1792 | Photobucket

 

[Masha]

Think about it. BB attaches to gravel in the same manner as it attaches to the bio-media in your filter. If water rushing through an HOB filter at 300 gallons per hour doesn't wash BB off the little "bio-rocks" (ie seachem matrix or equivalent) in an AquaClear 70, the BB sure isn't going to be "washed off" the gravel with the speed of water flowing into a siphon.

!! That's an excellent point.