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I have a green C. Wendtii and they are showing the upward roots. At first I was surprised that thin roots are growing upwards and I thought the water current was too strong - I planted them in the aquarium near the filter where the water flow is upwards.

I researched about it and what I got is that (1) the Crypts are said to be drawing nutrients directly from the water itself and (2) my substrate lacks nutrients. On the former explanation it does seem to make sense but on the latter - i believe my substrate has a very rich nutrients. It has three layers from top to bottom: very fine river sediments, fine gravel then garden soil.

I believe the upward roots are partly for self defence against fish disturbing the plants. I have Corydoras and they love to stick their face into the sand and because of that they have successfully uprooted a few of my plants - save for the Crypts. I have seen my Corydoras and other fish trying to go near the Crypts' main stem in search for food but they can't due to the upward roots - and I am actually surprised that those thin roots are actually quite sturdy. It is like a barrier.

My apology for the lengthy post. :p The image below is a previous photo of my tank. The stems now are almost impenetrable due to the upward roots.
 

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I doubt roots are growing upwards because a lack of nutrients. The plant can obtain it's nutrients from the water column through its leaves so why would it send roots up. This is only compounded with you saying you have a rich substrate.
Not sure what's causing this unfortunately hopefully someone else with more experience can chime in.


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