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"When I was searching about this topic I came across a paper that measured beneficial bacteria in the tank (it was really focused on substrate vs filter) and it found that the bulk of the bacteria was in the filter in material like the sponge and the substrate didn't have that much."

I'm guessing that this paper dealt with typical tank containing a gravel or sand substrate. If so, there would be very little bacterial activity of any kind in the substrate. In contrast, a gram of soil contains Zillions of bacteria.

Jake37's tank has nice plant growth, good lighting and floating plants. Could be the reason his nitrates are so low. Frankly, I don't see that much plant growth in the Chinese bowl. Window light may not be enough.

I'm running all of my 8 tanks without filters. Plants, fish, and shrimp are all doing really well. Nitrates are zero.

Goal for NPT tanks is to encourage enough plant growth to remove the ammonia before it's converted to nitrates. Nitrification competes with plants and reduces their growth. Denitrification is not that efficient and it produces nitrites. Folks, let's keep the focus on plant growth, not filters and denitrification.
 

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Light spectra can influence the production of aerial leaves in aquatic plants. Dr. Wetzel (p. 526) and other aquatic botanists say that a low R/FR, meaning a low ratio of 660 nm (Red) light to 730 nm (Far Red) light, will induce emergent growth such as occurs in shallow water. That's because water preferentially absorbs 730 nm (Far Red light), thereby increasing red light (660 nm). This is a hormonal trigger thingy.

Also, low CO2 will also induce aerial leaves.

My water lily of 3 weeks age has already sent up an aerial leaf and threatens to send up a couple more. I think it's because of the lighting I have been using, which is outdoor evening light plus LED lamp where half of the LEDs are red. John's lighting setup probably has a totally different spectra.

That said, many hobbyists prefer that their tank Nymphaea don't send up floating leaves.
 

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The packing material that you used to grow the lily looks more like peat moss than clay.

Google Search: Moss peat is a bryophyte also called sphagnum or bog moss. Because of the presence of a remarkable water holding capacity moss peat is used as a packing material in the transportation of flowers, live plants, tubers, bulbs, seedlings, etc.

That would explain the slow growth. Peat moss is a very poor substrate. Too acidic, too "fluffy", lacks iron, etc. Even if you add fertilizers, it will never be as good as ordinary garden soil. Bagged potting soil would be my second choice.

I enjoy your poetry.
 

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Only noting an uptick in ammonia readings, 0.25ppms. Shouldn't be too surprising since it's been 3 months since the last partial water change. Immediately did about a 25% WC (I try to keep about 8 liters of conditioned water always on hand.)
Was that photo taken before the water change or afterwards? It looks like the water is tea-colored due to tannin accumulation.
 

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The tannins that cause that tea-color will inhibit bacterial growth. That almost surely includes nitrifying bacteria, which could explain the ammonia in your bowl. Tannin release by the potting soil organic matter should decrease over time. In the meantime, I would change the water to remove the tannins. Here's one article from a quick Google search 'Tannins and Bacteria': Tannins as an alternative to antibiotics
 

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Bowl is beautiful and I love the surrounding arrangement.
I don't think that the bowl will support many fish and oxygen deficiency is a possibility.
You mentioned keeping plant debris to produce CO2. I would not do that--at least purposefully-- for this small setup (no aeration and few or no submerged plants to produce oxygen). Emergent plants get their CO2 from air.
I would remove excess debris and not add more fish (i.e., do not increase your stocking density).
The algae growth you see fortuitously plays the role of submerged plants. It oxygenates the water. In this situation, algae is a bonus!
Note: It is refreshing that you have such interest in ecosystem processes and are sharing your observations with us.
 

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The Sag don't look good, covered with algae and probably dying, making the substrate go bad. They're at the bottom where there isn't much light. Ideally, these small plants should be in a shallow tank where they can get the light they need. For this situation, plants with longer leaves or stems might be a better choice than Sagattaria subulata. Cryptocoryne balansae, Val, Sagittaria graminea?
Or you could just dedicate bowl to the RTL. I would hand remove some of that hair algae and trim off leaves that are hopelessly infested with algae.

Looks like the emergent plants are doing great!
 

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Those little Sag are competing with big houseplants and floating plants, which all have the 'aerial advantage'.
In another thread, you mentioned removing houseplants from your Apistogramma tank. The results from that maneuver should be instructive for this situation.
 
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